Diff of the two buildlogs: -- --- b1/build.log 2025-03-09 18:14:03.580118869 +0000 +++ b2/build.log 2025-03-09 19:27:21.462099746 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Mar 9 05:14:23 -12 2025 -I: pbuilder-time-stamp: 1741540463 +I: Current time: Sun Apr 12 14:37:08 +14 2026 +I: pbuilder-time-stamp: 1775954228 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -35,52 +35,84 @@ dpkg-source: info: applying disable_riscv64_timeout_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2513156/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 12 00:37 /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/2068256/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='6d016b4e356a43bba37eda0559d0aad5' - 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='2513156' - PS1='# ' - PS2='> ' + INVOCATION_ID=23f6d0e8df474f4993cdeda5b5b40615 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2068256 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.PfaUNweg/pbuilderrc_R0Lm --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.PfaUNweg/b1 --logfile b1/build.log rdkit_202409.6-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.PfaUNweg/pbuilderrc_B6tE --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.PfaUNweg/b2 --logfile b2/build.log rdkit_202409.6-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2513156/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -572,7 +604,7 @@ Get: 367 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2024.20250114-1 [8760 kB] Get: 368 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2024.20250114-1 [17.1 MB] Get: 369 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2024.20250114-1 [24.7 MB] -Fetched 396 MB in 3s (148 MB/s) +Fetched 396 MB in 3s (131 MB/s) Preconfiguring packages ... Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19897 files and directories currently installed.) @@ -1758,8 +1790,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Mar 9 17:16:43 UTC 2025. -Universal Time is now: Sun Mar 9 17:16:43 UTC 2025. +Local time is now: Sun Apr 12 00:39:41 UTC 2026. +Universal Time is now: Sun Apr 12 00:39:41 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-4.1+b1) ... @@ -1924,11 +1956,6 @@ Setting up pandoc (3.1.11.1+ds-2) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up ssl-cert (1.1.3) ... -hostname: Name or service not known -make-ssl-cert: Could not get FQDN, using 'codethink04-arm64'. -make-ssl-cert: You may want to fix your /etc/hosts and/or DNS setup and run -make-ssl-cert: 'make-ssl-cert generate-default-snakeoil --force-overwrite' -make-ssl-cert: again. Setting up libboost-date-time1.83-dev:arm64 (1.83.0-4.1+b1) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up shared-mime-info (2.4-5+b2) ... @@ -2148,7 +2175,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202409.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202409.6-2_source.changes +I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2068256/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202409.6/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202409.6-2_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202409.6-2 dpkg-buildpackage: info: source distribution unstable @@ -2272,8 +2303,8 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (4.8s) --- Generating done (2.0s) +-- Configuring done (3.4s) +-- Generating done (1.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -2334,7 +2365,7 @@ command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (1.6s) +-- Configuring done (1.1s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/build-17 make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' @@ -2348,100 +2379,100 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend +make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend +make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend +make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend +make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/INCHI-API /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake "--color=" -make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/CoordGen /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake "--color=" -make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend +make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/RingFamilies /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/RingFamilies /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake "--color=" -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/GA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA/CMakeFiles/ga.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/rdkitCatch.dir/DependInfo.cmake "--color=" -make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDStreams /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/DependInfo.cmake "--color=" +make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build +make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202409.6/External/INCHI-API/python/inchi.py /build/reproducible-path/rdkit-202409.6/rdkit/Chem/inchi.py -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build -make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build -[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build make[4]: Nothing to be done for 'External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Invariant.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/build +make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o -MF CMakeFiles/RDGeneral.dir/types.cpp.o.d -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/types.cpp +make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/utils.cpp -make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend -[ 1%] Built target inchi_support -[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Invariant.cpp +make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -MF CMakeFiles/ga.dir/ga/StringChromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/StringChromosome.cpp -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_main.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDStreams /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams/CMakeFiles/RDStreams.dir/DependInfo.cmake "--color=" -[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake "--color=" -[ 1%] Built target coordgen_support -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/Chromosome.cpp -[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -[ 1%] Built target ringdecomposerlib_support -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/IntegerStringChromosomePolicy.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDGeneralExceptions.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o -MF CMakeFiles/RDGeneral.dir/types.cpp.o.d -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/types.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build +[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_main.cpp +[ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -MF CMakeFiles/ga.dir/ga/StringChromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/StringChromosome.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/StringChromosome.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/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-202409.6/Code/ML/Cluster/Murtagh/hc.c +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/utils.cpp +[ 1%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_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 -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDStreams/streams.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDGeneralExceptions.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/RDLog.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 1%] Built target coordgen_support +[ 1%] Built target inchi_support +[ 1%] Built target ringdecomposerlib_support [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/LocaleSwitcher.cpp -[ 1%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_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 -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDStreams/streams.cpp -[ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/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-202409.6/Code/ML/Cluster/Murtagh/hc.c +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/Chromosome.cpp [ 1%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/Cluster/Murtagh/hcdriver.c +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/IntegerStringChromosomePolicy.cpp [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,--dependency-file=CMakeFiles/hc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2024.09.6 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2024.09.6 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/BinaryStringChromosomePolicy.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_BOOST_STACKTRACE -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/versions.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 1%] Built target hc +[ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/ga/BinaryStringChromosomePolicy.cpp [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/util/RandomUtil.cpp -[ 1%] Built target hc [ 1%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/GA/util/Util.cpp [ 1%] Linking CXX static library librdkitCatch.a @@ -2457,6 +2488,12 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2024.09.6 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 2%] Built target ga +[ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2024.09.6 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 2%] Built target RDStreams [ 2%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDGeneral.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 @@ -2468,193 +2505,187 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDBoost /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.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-202409.6/obj-aarch64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVect.cpp +[ 2%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" +[ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitVect.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -[ 3%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/DataStructs/SparseBitVect.cpp -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend +make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/ExplicitBitVect.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake "--color=" [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Utils.cpp +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/ExplicitBitVect.cpp [ 3%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/python3.13 -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDBoost/Wrap.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/testConcurrentQueue.cpp +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/testDict.cpp -[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/testRDValue.cpp -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/base64.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_dict.cpp -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitOps.cpp -[ 3%] Linking CXX shared library ../../lib/libRDKitRDStreams.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDStreams.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2024.09.6 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Utils.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 3%] Built target RDStreams -make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/base64.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/testRDValue.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_dict.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/catch_logs.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/testConcurrentQueue.cpp +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/BitOps.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/DataStructs/DiscreteDistMat.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/DataStructs/DiscreteValueVect.cpp +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/FPBReader.cpp [ 3%] Linking CXX executable testConcurrentQueue cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testConcurrentQueue.dir/link.d CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 3%] Built target testConcurrentQueue make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake "--color=" +[ 3%] Built target testConcurrentQueue +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Catalogs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/FPBReader.cpp [ 3%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -MF CMakeFiles/testMatrices.dir/testMatrices.cpp.o.d -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/testMatrices.cpp -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/DataStructs/MultiFPBReader.cpp +[ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Catalogs/Catalog.cpp [ 3%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/EigenSolvers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 3%] Built target EigenSolvers -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Catalogs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Catalogs/Catalog.cpp -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.cpp -[ 4%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogParams.cpp -[ 4%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Catalogs/CatalogEntry.cpp make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Query /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Query /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 5%] Linking CXX executable logTestsCatch -[ 5%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o +[ 3%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Query && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Query/CMakeFiles/testQuery.dir/test.cpp.o -MF CMakeFiles/testQuery.dir/test.cpp.o.d -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Query/test.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 -[ 5%] Linking CXX shared library ../../lib/libRDKitRDBoost.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 5%] Built target logTestsCatch +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/DataStructs/MultiFPBReader.cpp +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/RealValueVect.cpp make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o +[ 3%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDBoost.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2024.09.6 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so +[ 4%] Linking CXX executable logTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/logTestsCatch.dir/link.d CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 4%] Built target logTestsCatch make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 5%] Built target RDBoost +[ 4%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/SimDivPickers/DistPicker.cpp +[ 4%] Linking CXX shared library ../../lib/libRDKitRDBoost.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDBoost.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2024.09.6 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 4%] Built target RDBoost make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake "--color=" -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/SimDivPickers/DistPicker.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 6%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o +[ 5%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/RDBoost/Wrap/RDBase.cpp -[ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2024.09.6 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so +[ 5%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 6%] Built target Catalogs +[ 5%] Built target dictTestsCatch make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 6%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o +[ 5%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DClustering_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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/Cluster/Murtagh/Clustering.cpp -[ 6%] Linking CXX executable dictTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 -[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o +[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/SimDivPickers/MaxMinPicker.cpp -[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/SimDivPickers/HierarchicalClusterPicker.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/dictTestsCatch.dir/link.d CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/libCatch2.a /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 6%] Built target dictTestsCatch +[ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Catalogs/CatalogParams.cpp +[ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Catalogs/CatalogEntry.cpp [ 7%] Linking CXX executable testMatCalc cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/SimDivPickers/HierarchicalClusterPicker.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatCalc.dir/link.d CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 7%] Built target testMatCalc +[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Catalogs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2024.09.6 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 7%] Built target Catalogs [ 7%] Linking CXX executable testMatrices cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMatrices.dir/link.d CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -2662,13 +2693,8 @@ [ 7%] Built target testMatrices [ 7%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 -[ 7%] Linking CXX executable testRDValue -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2024.09.6 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o CMakeFiles/DataStructs.dir/RealValueVect.cpp.o ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDValue.dir/link.d CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 7%] Built target testRDValue make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 7%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend @@ -2676,54 +2702,66 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake "--color=" make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/catchDataStructs.dir/DependInfo.cmake "--color=" -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build [ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/point.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/DataStructs/CMakeFiles/catchDataStructs.dir/build.make Code/DataStructs/CMakeFiles/catchDataStructs.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 7%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/DataStructs/testFPB.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/point.cpp +[ 7%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o +[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/DataStructs/testDatastructs.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Geometry/Transform2D.cpp [ 7%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o +[ 7%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/testMultiFPB.cpp -[ 7%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -[ 7%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/DataStructs/testFPB.cpp [ 8%] Building CXX object Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/DataStructs/testDatastructs.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -MF CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o.d -o CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/catch_tests.cpp +[ 8%] Linking CXX executable testQuery +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 +[ 8%] Linking CXX executable testRDValue +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDValue.dir/link.d CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testQuery.dir/link.d CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 8%] Built target testRDValue +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend +[ 8%] Built target testQuery +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -MF CMakeFiles/cDataStructs.dir/DataStructs.cpp.o.d -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/DataStructs.cpp [ 8%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp @@ -2741,13 +2779,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 9%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/InfoBitRanker.cpp -[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Geometry/Transform2D.cpp -[ 9%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testQuery.dir/link.d CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 9%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/Clustering.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 9%] Built target testQuery +[ 9%] Built target Clustering make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake "--color=" @@ -2756,13 +2792,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 10%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/testPickers.cpp -[ 10%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 [ 10%] Linking CXX executable testDict cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/Clustering.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDict.dir/link.d CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 10%] Built target Clustering +[ 10%] Built target testDict make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake "--color=" @@ -2771,45 +2805,51 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 10%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/SimDivPickers/catch_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDict.dir/link.d CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Geometry/Transform3D.cpp +[ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Geometry/UniformGrid3D.cpp +[ 11%] Linking CXX executable catchDataStructs +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/catchDataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/catchDataStructs.dir/link.d CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -o catchDataStructs ../RDGeneral/librdkitCatch.a ../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 10%] Built target testDict +[ 11%] Built target catchDataStructs make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o +[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/MaxMinPicker.cpp -[ 10%] Linking CXX executable catchDataStructs -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/catchDataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/catchDataStructs.dir/link.d CMakeFiles/catchDataStructs.dir/catch_tests.cpp.o -o catchDataStructs ../RDGeneral/librdkitCatch.a ../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 10%] Built target catchDataStructs -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Geometry/Transform3D.cpp -[ 11%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so +[ 12%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/InfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2024.09.6 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2024.09.6 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 11%] Built target InfoTheory +[ 12%] Built target InfoTheory +[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/LeaderPicker.cpp +[ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformRealValueGrid3D.cpp +[ 12%] Linking CXX executable testSimDivPickers +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSimDivPickers.dir/link.d CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2024.09.6 ../../lib/libRDKithc.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 12%] Built target testSimDivPickers make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 11%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o +[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp -[ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/Geometry/UniformGrid3D.cpp -[ 12%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMetricMatrixCalc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 12%] Linking CXX executable testFPB +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFPB.dir/link.d CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 12%] Built target rdMetricMatrixCalc +[ 12%] Built target testFPB make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ML/Data /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Data /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake "--color=" @@ -2818,267 +2858,262 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 12%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Data && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/Data/cQuantize.cpp -[ 12%] Linking CXX executable testSimDivPickers -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSimDivPickers.dir/link.d CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2024.09.6 ../../lib/libRDKithc.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 12%] Built target testSimDivPickers -[ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/UniformRealValueGrid3D.cpp -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/DiscreteValueVect.cpp -[ 12%] Linking CXX executable testFPB -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFPB.dir/link.d CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 12%] Built target testFPB [ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/GridUtils.cpp -[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/LeaderPicker.cpp [ 13%] Linking CXX executable pickersTestsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickersTestsCatch.dir/link.d CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 13%] Built target pickersTestsCatch -[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp +[ 13%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 13%] Linking CXX executable testMultiFPB cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultiFPB.dir/link.d CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 13%] Built target testMultiFPB -[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp -[ 13%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp -[ 13%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp -[ 13%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/SparseIntVect.cpp +[ 13%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMetricMatrixCalc.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 13%] Built target rdMetricMatrixCalc +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/RealValueVect.cpp +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_SparseBV.cpp +[ 14%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDGeometryLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Built target RDGeometryLib +[ 14%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Atom.cpp -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryAtom.cpp -[ 13%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +[ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp +[ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp +[ 14%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 14%] Built target cQuantize make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cQuantize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build -[ 13%] Built target cQuantize make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 14%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/AlignPoints.cpp +[ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake "--color=" -[ 13%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/AlignPoints.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o +[ 14%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/testTransforms.cpp +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_BitOps.cpp +[ 14%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_FPB.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2024.09.6 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 14%] Built target Alignment make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o +[ 14%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/Geometry/testGrid.cpp -[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/SparseIntVect.cpp -[ 13%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Alignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2024.09.6 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so +[ 14%] Linking CXX executable testDataStructs +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDataStructs.dir/link.d CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Built target Alignment +[ 14%] Built target testDataStructs make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testRealValueGrid.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Geometry/CMakeFiles/testRealValueGrid.dir/build.make Code/Geometry/CMakeFiles/testRealValueGrid.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Building CXX object Code/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o +[ 14%] Building CXX object Code/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -MF CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o.d -o CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/testRealValueGrid.cpp +[ 14%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKithc.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 14%] Built target rdSimDivPickers make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o +[ 14%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/catch_tests.cpp +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_Utils.cpp +[ 14%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdInfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 14%] Built target rdInfoTheory make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o +[ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/Point.cpp -[ 13%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 -[ 13%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDataStructs.dir/link.d CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 14%] Linking CXX executable testTransforms +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTransforms.dir/link.d CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Built target testDataStructs +[ 14%] Built target testTransforms make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o +[ 14%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/testConrec.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSimDivPickers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKithc.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryAtom.cpp +[ 14%] Linking CXX executable testGrid +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGrid.dir/link.d CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 13%] Built target rdSimDivPickers +[ 14%] Built target testGrid make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 14%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o +[ 15%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/testAlignment.cpp -[ 14%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdInfoTheory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 15%] Linking CXX executable geometryTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/geometryTestsCatch.dir/link.d CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 14%] Built target rdInfoTheory +[ 15%] Built target geometryTestsCatch make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 14%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o +[ 15%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/Wrap/rdAlignment.cpp -[ 14%] Linking CXX executable testGrid -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGrid.dir/link.d CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 15%] Linking CXX executable testRealValueGrid +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRealValueGrid.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRealValueGrid.dir/link.d CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -o testRealValueGrid ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 14%] Built target testGrid +[ 15%] Built target testRealValueGrid make -f Code/Features/CMakeFiles/testBaseFeatures.dir/build.make Code/Features/CMakeFiles/testBaseFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Features /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Features /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Features/CMakeFiles/testBaseFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/Features/CMakeFiles/testBaseFeatures.dir/build.make Code/Features/CMakeFiles/testBaseFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 14%] Building CXX object Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o +[ 15%] Building CXX object Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Features && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Features/CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Features/testFeatures.cpp -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryBond.cpp -[ 14%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTransforms.dir/link.d CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 14%] Built target testTransforms make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 14%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o +[ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/FreeChemicalFeature.cpp -[ 14%] Linking CXX executable geometryTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/geometryTestsCatch.dir/link.d CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryBond.cpp +[ 15%] Linking CXX executable testAlignment +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAlignment.dir/link.d CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 14%] Built target geometryTestsCatch -[ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/UniformGrid3D.cpp -[ 15%] Linking CXX executable testRealValueGrid -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRealValueGrid.dir/link.txt --verbose=1 +[ 15%] Built target testAlignment [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Bond.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRealValueGrid.dir/link.d CMakeFiles/testRealValueGrid.dir/testRealValueGrid.cpp.o -o testRealValueGrid ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 16%] Linking CXX executable testConrec +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testConrec.dir/link.d CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 15%] Built target testRealValueGrid -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o +[ 16%] Built target testConrec +[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/UniformGrid3D.cpp +[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolOps.cpp -[ 15%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +[ 17%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2024.09.6 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2024.09.6 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 15%] Built target ChemicalFeatures +[ 17%] Built target ChemicalFeatures make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +[ 17%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -MF CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o.d -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/testChemicalFeatures.cpp -[ 15%] Linking CXX executable testAlignment -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAlignment.dir/link.d CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 15%] Built target testAlignment -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp -[ 15%] Linking CXX executable testBaseFeatures +[ 17%] Linking CXX executable testBaseFeatures cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Features && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBaseFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testBaseFeatures.dir/link.d CMakeFiles/testBaseFeatures.dir/testFeatures.cpp.o -o testBaseFeatures ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 15%] Built target testBaseFeatures -[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/RealValueVect.cpp -[ 16%] Linking CXX executable testConrec -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testConrec.dir/link.d CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 16%] Built target testConrec -[ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_SparseBV.cpp +[ 17%] Built target testBaseFeatures +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp [ 17%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAlignment.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 17%] Built target rdAlignment -[ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ROMol.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RWMol.cpp [ 17%] Linking CXX executable testChemicalFeatures cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemicalFeatures.dir/link.d CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/PeriodicTable.cpp +[ 18%] Built target testChemicalFeatures +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/atomic_data.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/QueryOps.cpp /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FindRings.cpp:1292:36: warning: unused parameter 'mol' [-Wunused-parameter] 1292 | void findRingFamilies(const ROMol &mol) { | ~~~~~~~~~~~~~^~~ -[ 17%] Built target testChemicalFeatures -[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/UniformRealValueGrid3D.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ROMol.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RWMol.cpp -[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/rdGeometry.cpp -[ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_BitOps.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/PeriodicTable.cpp -[ 18%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_FPB.cpp In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/stl_tree.h:63, from /usr/include/c++/14/map:62, @@ -3091,19 +3126,15 @@ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/atomic_data.cpp -[ 18%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/wrap_Utils.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/QueryOps.cpp -[ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 18%] Built target rdGeometry +[ 18%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/rdGeometry.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolPickler.cpp +[ 18%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cDataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 18%] Built target cDataStructs [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Canon.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o @@ -3116,6 +3147,11 @@ /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolPickler.cpp:72:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 72 | if (res < 0) { | ~~~~^~~ +[ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/UniformRealValueGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 18%] Built target rdGeometry [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Kekulize.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o @@ -3124,12 +3160,12 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/AddHs.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Matrices.cpp -[ 19%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Chirality.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RingInfo.cpp +[ 19%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdBase.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 19%] Built target rdBase @@ -3139,11 +3175,6 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Renumber.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/AdjustQuery.cpp -[ 19%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/cDataStructs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/RealValueVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 19%] Built target cDataStructs [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Resonance.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o @@ -3178,151 +3209,137 @@ make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/tableTestsCatch.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 20%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/MolTransforms.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build [ 20%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o +make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build -[ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/GenericGroups.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParse.cpp -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/tableTestsCatch.dir/DependInfo.cmake "--color=" +[ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/GenericGroups.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmilesParseOps.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/Trajectory.cpp -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmartsWrite.cpp +[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/Trajectory.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPMol.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SmilesParse/SmilesWrite.cpp +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/SmartsWrite.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/tableTestsCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -[ 21%] Building CXX object Code/GraphMol/CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/tableTestsCatch.dir/catch_periodictable.cpp.o -MF CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o.d -o CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_periodictable.cpp -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/Subgraphs.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Digraph.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/Node.cpp -[ 22%] Linking CXX executable tableTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/tableTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tableTestsCatch.dir/link.d CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o -o tableTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitGraphMol.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 22%] Built target tableTestsCatch -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o +[ 21%] Building CXX object Code/GraphMol/CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/tableTestsCatch.dir/catch_periodictable.cpp.o -MF CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o.d -o CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_periodictable.cpp +[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/Subgraphs.cpp +[ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerCharges.cpp -[ 22%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Trajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 22%] Built target Trajectory +[ 21%] Built target Trajectory make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 22%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o +[ 21%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/Edge.cpp -[ 22%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/SubgraphUtils.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Sort.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CXSmilesOps.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -MF CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o.d -o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp -[ 22%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +[ 21%] Linking CXX executable tableTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/tableTestsCatch.dir/link.txt --verbose=1 +[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Digraph.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tableTestsCatch.dir/link.d CMakeFiles/tableTestsCatch.dir/catch_periodictable.cpp.o -o tableTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitGraphMol.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 22%] Built target MolTransforms +[ 21%] Built target tableTestsCatch make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 23%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o +[ 22%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Parser.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so +[ 22%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerParams.cpp +[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CXSmilesOps.cpp +[ 22%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/SubgraphUtils.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/Node.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/Edge.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Sort.cpp +[ 24%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogParams.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -MF CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o.d -o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/CanonicalizeStereoGroups.cpp +[ 24%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 +[ 24%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 23%] Built target GenericGroups +[ 24%] Built target MolTransforms make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so +[ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNParse.cpp -[ 23%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/GasteigerParams.cpp -[ 24%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/MolCatalogParams.cpp -[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smarts.tab.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 24%] Built target MolCatalog +[ 24%] Built target PartialCharges make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake "--color=" @@ -3331,121 +3348,134 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdqueries.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 24%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Subgraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so +[ 24%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +[ 24%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GenericGroups.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 24%] Built target Subgraphs +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +[ 24%] Built target GenericGroups make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o +[ 24%] Built target MolCatalog cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Trajectory.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp -[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smiles.tab.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 25%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/PartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 25%] Built target PartialCharges make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 25%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o +[ 24%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/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-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 25%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Queries.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smarts.tab.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smiles.tab.cpp +[ 24%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Subgraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 24%] Built target Subgraphs make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 25%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o +[ 24%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructMatch.cpp -[ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructUtils.cpp -[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/lex.yysmarts.cpp -[ 26%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +[ 24%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 27%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o +[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Queries.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/lex.yysmarts.cpp +[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/lex.yysmiles.cpp +[ 26%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdTrajectory.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNAttribs.cpp +[ 26%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Writer.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 27%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemicalFeatures.dir/link.d -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.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 27%] Built target rdChemicalFeatures make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake "--color=" +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' [ 27%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/BFGSOpt.cpp +[ 27%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/LinearSearch.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 27%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp -[ 27%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/SLNAttribs.cpp -[ 28%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdTrajectory.cpp -[ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/LinearSearch.cpp -[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule6.cpp -[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SLNParse/sln.tab.cpp -[ 28%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2024.09.6 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 28%] Built target Optimizer +[ 27%] Built target rdtrajectory make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +[ 27%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o +[ 27%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdtrajectory.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 28%] Built target rdtrajectory +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 28%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/SubstructUtils.cpp make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake "--color=" @@ -3454,14 +3484,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp -[ 28%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Writer.cpp -[ 28%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/CIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 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/configs/AtropisomerBond.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.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so +[ 28%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Optimizer.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2024.09.6 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 28%] Built target CIPLabeler +[ 28%] Built target Optimizer make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake "--color=" @@ -3470,21 +3498,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp -[ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemicalFeatures.dir/link.d -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.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 28%] Built target rdChemicalFeatures make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake "--color=" @@ -3493,6 +3506,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/Numerics/Optimizer/testOptimizer.cpp +[ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 +[ 28%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SmilesParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/CanonicalizeStereoGroups.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' @@ -3505,54 +3522,44 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/ForceField.cpp -[ 29%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/lex.yysln.cpp -[ 29%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +[ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/SLNParse/sln.tab.cpp +[ 28%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 +[ 28%] Linking CXX executable testOptimizer +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testOptimizer.dir/link.d CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 29%] Built target SubstructMatch +[ 28%] Built target testOptimizer make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o +[ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/cptest.cpp -[ 29%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp -[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdPartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 30%] Built target rdPartialCharges -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/querytest.cpp -[ 30%] Linking CXX executable testOptimizer -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 -[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraint.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testOptimizer.dir/link.d CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/CIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 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/configs/AtropisomerBond.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.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 30%] Built target testOptimizer +[ 28%] Built target CIPLabeler make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o +[ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/itertest.cpp -[ 31%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 +[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.cpp +[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdPartialCharges.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 31%] Built target rdPartialCharges make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" @@ -3561,22 +3568,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 31%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/memtest1.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 31%] Built target rdqueries -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -MF CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o.d -o CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_moliterators.cpp -[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 31%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 31%] Built target rdCIPLabeler +[ 31%] Built target ShapeHelpers make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" @@ -3585,163 +3582,125 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 31%] Building CXX object Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_queries.cpp -[ 31%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraint.cpp +[ 31%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +[ 31%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdqueries.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 31%] Built target SLNParse +[ 31%] Built target MolInterchange make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend +[ 31%] Built target rdqueries make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/catch_molbundle.cpp -[ 31%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 -[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 31%] Built target ShapeHelpers make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build +[ 31%] Building CXX object Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/catch_molbundle.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/SmilesParse/test2.cpp +[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 31%] Built target rdMolTransforms -make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FilterCatalog/Filters.cpp -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -MF CMakeFiles/ForceField.dir/AngleConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/AngleConstraints.cpp -[ 32%] Linking CXX executable graphmolcpTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolcpTest.dir/link.d CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target graphmolcpTest -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -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-202409.6/obj-aarch64-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.cpp -[ 32%] Linking CXX executable moliteratorTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 -[ 32%] Linking CXX executable graphmolIterTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target moliteratorTestsCatch -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smatest.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolIterTest.dir/link.d CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target graphmolIterTest make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o +[ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/v2smiTestCatch.dir/v2catch_tests.cpp.o -MF CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o.d -o CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/v2catch_tests.cpp -[ 32%] Linking CXX executable smiTest2 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraint.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest2.dir/link.d CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 31%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolcpTest.dir/link.d CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target smiTest2 +[ 31%] Built target graphmolcpTest make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" -[ 32%] Linking CXX executable graphmolMemTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o +[ 31%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o -MF CMakeFiles/testSubgraphs1.dir/test1.cpp.o.d -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/test1.cpp -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMemTest1.dir/link.d CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.cpp +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/PositionConstraint.cpp +[ 31%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructMatch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target graphmolMemTest1 +[ 31%] Built target SubstructMatch make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o +[ 31%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/test2.cpp +[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target rdMolCatalog +[ 31%] Built target rdMolCatalog make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o +[ 31%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Subgraphs/catch_tests.cpp -[ 32%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalog.cpp -[ 32%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 -[ 32%] Linking CXX executable queryTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/queryTestsCatch.dir/link.d CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 32%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/lex.yysln.cpp +[ 32%] Linking CXX executable graphmolIterTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 +[ 32%] Linking CXX executable smiTest2 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolIterTest.dir/link.d CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest2.dir/link.d CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target queryTestsCatch -[ 32%] Built target MolInterchange +[ 32%] Built target graphmolIterTest make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend +[ 32%] Built target smiTest2 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 32%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp [ 32%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/PartialCharges/test1.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -[ 32%] Linking CXX executable molbundleTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molbundleTestsCatch.dir/link.d CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 32%] Linking CXX executable graphmolMemTest1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMemTest1.dir/link.d CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target molbundleTestsCatch +[ 32%] Built target graphmolMemTest1 make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake "--color=" @@ -3750,17 +3709,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 32%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -MF CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o.d -o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/DistanceConstraints.cpp -[ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/PatternFingerprints.cpp -[ 32%] Linking CXX executable graphmolqueryTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 -[ 32%] Linking CXX executable testPartialCharges -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/TorsionConstraint.cpp +[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleBend.cpp +[ 32%] Linking CXX executable queryTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/queryTestsCatch.dir/link.d CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target graphmolqueryTest +[ 32%] Built target queryTestsCatch make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake "--color=" @@ -3769,19 +3726,29 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 32%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPartialCharges.dir/link.d CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 32%] Linking CXX executable molbundleTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molbundleTestsCatch.dir/link.d CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -o molbundleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 32%] Built target testPartialCharges -[ 32%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/PositionConstraint.cpp +[ 32%] Built target molbundleTestsCatch +make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend +[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/UFF/BondStretch.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' +[ 32%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp [ 33%] Linking CXX executable v2smiTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2smiTestCatch.dir/link.d CMakeFiles/v2smiTestCatch.dir/v2catch_tests.cpp.o -o v2smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 33%] Built target v2smiTestCatch make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Nonbonded.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' @@ -3789,93 +3756,131 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_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 -DReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp +[ 33%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +[ 33%] Linking CXX executable testPartialCharges +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 [ 33%] Linking CXX executable subgraphsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/subgraphsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/subgraphsCatch.dir/link.d CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -o subgraphsCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPartialCharges.dir/link.d CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 33%] Built target subgraphsCatch +[ 33%] Built target testPartialCharges make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/subgraphsCatch.dir/link.d CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -o subgraphsCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp +[ 33%] Built target subgraphsCatch +make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake "--color=" +[ 33%] Linking CXX executable testSubgraphs1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 +[ 33%] Built target SLNParse +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build +[ 33%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Abbreviations.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 33%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubgraphs1.dir/link.d CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 33%] Built target testSubgraphs1 +make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 33%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/querytest.cpp [ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp [ 33%] Linking CXX executable testSubgraphs2 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversion.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubgraphs2.dir/link.d CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 33%] Built target testSubgraphs2 -make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/test.cpp -[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/TorsionConstraint.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversions.cpp +[ 33%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -MF CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o.d -o CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_moliterators.cpp [ 33%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatGenerator.cpp -[ 33%] Linking CXX executable testSubgraphs1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubgraphs1.dir/link.d CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp +[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 +[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/UFF/TorsionAngle.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCIPLabeler.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 33%] Built target testSubgraphs1 -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend +[ 34%] Built target rdCIPLabeler +make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build +make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp -[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/AngleBend.cpp -[ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.cpp -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FilterCatalog/Filters.cpp +[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/UFF/Params.cpp +[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 33%] Built target rdMolInterchange -make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend +[ 34%] Built target rdShapeHelpers +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build +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-202409.6/obj-aarch64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Abbreviations.cpp -[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Fingerprints.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 -[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/UFF/BondStretch.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 34%] Built target ReducedGraphs -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build +make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 34%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.cpp -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdShapeHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 34%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/smatest.cpp +[ 34%] Linking CXX executable moliteratorTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moliteratorTestsCatch.dir/link.d CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 34%] Built target rdShapeHelpers +[ 34%] Built target moliteratorTestsCatch make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake "--color=" @@ -3884,15 +3889,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/test1.cpp -[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp -[ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Utils.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Utils.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Utils.cpp +[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolInterchange.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 34%] Built target rdSLNParse +[ 34%] Built target rdMolInterchange make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake "--color=" @@ -3901,244 +3904,254 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 34%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp -[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairs.cpp -[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Nonbonded.cpp -[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.cpp -[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversion.cpp -[ 34%] Linking CXX executable smaTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smaTest1.dir/link.d CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 34%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp +[ 34%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp +[ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp +[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/MMFF/AngleBend.cpp +[ 34%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 34%] Built target smaTest1 -[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp +[ 34%] Built target MolAlign +make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 34%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/test.cpp +[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.cpp +[ 34%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalog.cpp [ 34%] Linking CXX executable testReducedGraphs cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReducedGraphs.dir/link.d CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 34%] Built target testReducedGraphs -[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Inversions.cpp -[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/UFF/TorsionAngle.cpp -[ 35%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp -[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/UFF/Params.cpp -[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/MACCS.cpp -[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 -[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatParams.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 35%] Built target rdReducedGraphs -[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragFPGenerator.cpp -[ 35%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 -[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Utils.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Utils.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/Utils.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so +make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 34%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp +[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.cpp +[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 34%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/OopBend.cpp +/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': +/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 27 | const MMFFStbn *mmffStbnParams) { + | ^ +[ 34%] Linking CXX executable graphmolqueryTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolqueryTest.dir/link.d CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 35%] Built target MolAlign +[ 34%] Built target graphmolqueryTest make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend -[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/MMFF/AngleBend.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 36%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o +[ 35%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -MF CMakeFiles/Depictor.dir/RDDepictor.cpp.o.d -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/RDDepictor.cpp -[ 36%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 -[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/BondStretch.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdReducedGraphs.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 36%] Built target MolChemicalFeatures +[ 35%] Built target rdReducedGraphs make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/CoordGen/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 37%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o +[ 36%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/CoordGen/Wrap/rdCoordGen.cpp -[ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.cpp -[ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/OopBend.cpp -[ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/MMFF/TorsionAngle.cpp -[ 37%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -[ 37%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so +[ 36%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Abbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2024.09.6 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so -[ 37%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 37%] Built target FilterCatalog -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend -/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': -/build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 27 | const MMFFStbn *mmffStbnParams) { - | ^ +[ 36%] Built target Abbreviations +make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 36%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp +[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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-202409.6/Code/ForceField/MMFF/TorsionAngle.cpp +[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragCatParams.cpp +[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Nonbonded.cpp +[ 36%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 36%] 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color=" -[ 37%] Built target Abbreviations make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" -[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o +[ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp +[ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSLNParse.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 39%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSLNParse.dir/link.d CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 39%] Built target testSLNParse -[ 39%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -[ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Nonbonded.cpp -[ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o +[ 37%] Built target rdSLNParse +[ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +[ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/Params.cpp -[ 39%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o +[ 37%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/EmbeddedFrag.cpp -[ 39%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +[ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/MorganFingerprints.cpp +[ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairs.cpp +[ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +[ 37%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 37%] Built target rdCoordGen +[ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp +[ 37%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FragCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 39%] Built target FragCatalog -make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 39%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -[ 39%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/DepictUtils.cpp -[ 39%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp -[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.cpp -[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp -[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp -[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +[ 37%] Built target FragCatalog +[ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp -[ 40%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdCoordGen.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 40%] Built target rdCoordGen -[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp -[ 40%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Templates.cpp -[ 41%] Linking CXX shared library ../../lib/libRDKitForceField.so +[ 38%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/MACCS.cpp +[ 38%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp +[ 38%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/DepictUtils.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2024.09.6 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/AngleConstraints.cpp.o CMakeFiles/ForceField.dir/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/DistanceConstraints.cpp.o CMakeFiles/ForceField.dir/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/Inversions.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/UFF/Utils.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Built target ForceField +[ 38%] Built target ForceField make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' 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-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o +[ 38%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MHFP.cpp +[ 39%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 +[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 +[ 39%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSLNParse.dir/link.d CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 39%] Built target testSLNParse +[ 39%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.cpp -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 39%] Built target rdAbbreviations +[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smaTest1.dir/link.d CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 39%] Built target smaTest1 +[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp +[ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FilterMatchers.cpp +[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +[ 40%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolChemicalFeatures.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Built target rdMolChemicalFeatures -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o +[ 40%] Built target rdMolChemicalFeatures +[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp +[ 40%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Templates.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/MorganGenerator.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.cpp +/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': +/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:419:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); + | ^ +[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdAbbreviations.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Built target rdAbbreviations -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +[ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp +[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.cpp -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/FingerprintUtil.cpp -[ 41%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +[ 40%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Depictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2024.09.6 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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Built target Depictor +[ 40%] Built target Depictor +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/INCHI-API /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API/CMakeFiles/RDInchiLib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f External/INCHI-API/CMakeFiles/RDInchiLib.dir/build.make External/INCHI-API/CMakeFiles/RDInchiLib.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o +[ 40%] Building CXX object External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDInchiLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDINCHILIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/CMakeFiles/RDInchiLib.dir/inchi.cpp.o -MF CMakeFiles/RDInchiLib.dir/inchi.cpp.o.d -o CMakeFiles/RDInchiLib.dir/inchi.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/INCHI-API/inchi.cpp -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp +[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleContribs.cpp make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o +[ 40%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ChemTransforms/ChemTransforms.cpp -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:419:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); - | ^ -[ 41%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/MolFragmenter.cpp make -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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o +[ 40%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' @@ -4146,40 +4159,86 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o +[ 40%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/hashfunctions.cpp -[ 41%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +[ 40%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/normalize.cpp +[ 40%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/MolFragmenter.cpp +[ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2024.09.6 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so +[ 40%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 40%] Built target Fingerprints +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 40%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FilterCatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 40%] Built target FilterCatalog +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp [ 41%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 +[ 41%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleContribs.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 41%] Built target ForceFieldHelpers make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build +make -f Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build.make Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/build +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2024.09.6 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so +[ 41%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistGeomUtils.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o [ 41%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/catch_tests.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap/ForceField.cpp -[ 41%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistGeomUtils.cpp +[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/catch_tests.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 41%] Built target MolHash make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake "--color=" @@ -4188,76 +4247,48 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp -[ 41%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Fingerprints.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2024.09.6 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Built target Fingerprints -make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInteractionFields_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERACTIONFIELDS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -MF CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o.d -o CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp [ 41%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RDInchiLib.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2024.09.6 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/aarch64-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2024.09.6 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 41%] Built target RDInchiLib -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.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-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 41%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp -[ 42%] Linking CXX executable ForceFieldsCatch +[ 41%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp +[ 42%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/TriangleSmooth.cpp +[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 42%] Built target rdDepictor +make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 42%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolInteractionFields_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERACTIONFIELDS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -MF CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o.d -o CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/MIFDescriptors.cpp +[ 43%] Linking CXX executable ForceFieldsCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/ForceFieldsCatch.dir/link.d CMakeFiles/ForceFieldsCatch.dir/catch_tests.cpp.o -o ForceFieldsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 42%] Built target ForceFieldsCatch +[ 43%] Built target ForceFieldsCatch make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 42%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o +[ 43%] Building CXX object External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdinchi_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -MF CMakeFiles/rdinchi.dir/pyInchi.cpp.o.d -o CMakeFiles/rdinchi.dir/pyInchi.cpp.o -c /build/reproducible-path/rdkit-202409.6/External/INCHI-API/Wrap/pyInchi.cpp -[ 42%] Linking CXX shared library ../../../lib/libRDKitMolHash.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 -[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2024.09.6 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 42%] Built target MolHash -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 42%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDepictor.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 42%] Built target rdDepictor -[ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/TriangleSmooth.cpp [ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/DistViolationContrib.cpp [ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o @@ -4266,144 +4297,140 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContrib.cpp [ 43%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/ChiralViolationContribs.cpp -[ 43%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInteractionFields.so.1 -o ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 43%] Built target MolInteractionFields -make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend +[ 43%] Built target rdMolHash +[ 43%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.6 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 43%] Built target DistGeometry +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 44%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 -[ 44%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +[ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp +[ 43%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/testDistGeom.cpp +[ 43%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/DistGeom.cpp +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 43%] Built target rdForceFieldHelpers +[ 43%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp +[ 43%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemTransforms.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 -[ 44%] Built target rdfiltercatalog -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 44%] Built target ChemTransforms +[ 43%] Built target ChemTransforms make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CDXMLParser.cpp -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/Mol2FileParser.cpp -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileParser.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceFieldHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 44%] Built target rdForceFieldHelpers -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupWriting.cpp -[ 44%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 -[ 45%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so +[ 44%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeometry.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2024.09.6 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContribs.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContribs.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdinchi.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 45%] Built target rdinchi +[ 44%] Built target rdinchi +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/Mol2FileParser.cpp +[ 44%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 45%] Built target DistGeometry -[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" +[ 44%] Built target testDistGeom +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileParser.cpp +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 +[ 44%] Linking CXX shared library ../../../lib/libRDKitMolInteractionFields.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInteractionFields.dir/link.txt --verbose=1 +[ 44%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp -[ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolHash.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolInteractionFields.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInteractionFields.so.1 -o ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 CMakeFiles/MolInteractionFields.dir/MIFDescriptors.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 44%] Built target rdMHFPFingerprint +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../lib/libRDKitMolInteractionFields.so.1 ../../../lib/libRDKitMolInteractionFields.so +[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupParsing.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Built target rdMolHash -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +[ 44%] Built target MolInteractionFields +make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make -f Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build.make Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/testDistGeom.cpp -[ 46%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 +[ 45%] Building CXX object Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMIF_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInteractionFields/Wrap/CMakeFiles/rdMIF.dir/rdMIF.cpp.o -MF CMakeFiles/rdMIF.dir/rdMIF.cpp.o.d -o CMakeFiles/rdMIF.dir/rdMIF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/rdMIF.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdForceField.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Built target rdForceField -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-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" +[ 45%] Built target rdForceField +[ 45%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolSGroupWriting.cpp +[ 45%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 +[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/DistGeom.cpp -[ 46%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDistGeom.dir/link.d CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 45%] Built target DistGeom +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileStereochem.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Built target testDistGeom -[ 46%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/DistGeomHelpers/Embedder.cpp +[ 46%] Built target rdFingerprintGenerator [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MolFileWriter.cpp -[ 46%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp -[ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMHFPFingerprint.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Built target rdMHFPFingerprint [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/SDMolSupplier.cpp -[ 46%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/SDWriter.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/DistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 46%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Built target DistGeom +[ 46%] Built target DistGeomHelpers [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/SmilesWriter.cpp -[ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFingerprintGenerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Built target rdFingerprintGenerator [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/TDTMolSupplier.cpp [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/TDTWriter.cpp -[ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMIF.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMIF.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMIF.so CMakeFiles/rdMIF.dir/rdMIF.cpp.o ../../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 46%] Built target rdMIF [ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/TplFileParser.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o @@ -4416,12 +4443,11 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/CMLWriter.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/XYZFileWriter.cpp -[ 47%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/DistGeomHelpers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMIF.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMIF.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMIF.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMIF.so CMakeFiles/rdMIF.dir/rdMIF.cpp.o ../../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 47%] Built target DistGeomHelpers +[ 47%] Built target rdMIF [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/FileParsers/XYZFileParser.cpp [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o @@ -4444,6 +4470,11 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfiltercatalog.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 48%] Built target rdfiltercatalog [ 48%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FileParsers.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -4451,99 +4482,99 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 48%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/CoordGen /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake "--color=" make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/External/CoordGen /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake "--color=" [ 48%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_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-202409.6/External/CoordGen/test.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build -[ 48%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/testUFFForceField.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build -[ 48%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o +[ 48%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/UFF/testUFFForceField.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/testMMFFForceField.cpp make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 48%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/testMMFFForceField.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" -[ 48%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/test1.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/molopstest.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testChirality.cpp make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +[ 50%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/molopstest.cpp -[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/test1.cpp -[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testPickler.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testChirality.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" -[ 50%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 50%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testPicklerGlobalSettings.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testPickler.cpp -[ 49%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testPicklerGlobalSettings.cpp -[ 50%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/hanoitest.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build -[ 50%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testMolBundle.cpp +[ 50%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/hanoitest.cpp [ 50%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/resMolSupplierTest.cpp +[ 50%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testMolBundle.cpp [ 51%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/testSGroup.cpp [ 51%] Linking CXX executable molBundleTest @@ -4585,11 +4616,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o.d -o CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_organometallics.cpp -[ 51%] Linking CXX executable testCoordGen -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoordGen.dir/link.d CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 51%] Built target testCoordGen +[ 51%] Built target hanoiTest make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" @@ -4598,11 +4629,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_sgroups.cpp -[ 51%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/hanoiTest.dir/link.d CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable testUFFForceField +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceField.dir/link.d CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 51%] Built target hanoiTest +[ 51%] Built target testUFFForceField make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" @@ -4611,11 +4642,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_adjustquery.cpp -[ 51%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceField.dir/link.d CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable testCoordGen +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoordGen.dir/link.d CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 51%] Built target testUFFForceField +[ 51%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" @@ -4663,21 +4694,21 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 51%] Building CXX object Code/GraphMol/CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/molopsTestsCatch.dir/catch_molops.cpp.o -MF CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o.d -o CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/catch_molops.cpp -[ 51%] Linking CXX executable graphmolSGroupCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolSGroupCatch.dir/link.d CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 51%] Linking CXX executable graphmolTest1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 +[ 52%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTest1.dir/link.d CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 51%] Built target graphmolSGroupCatch +[ 52%] Built target graphmolTest1 make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 52%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o +[ 53%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/smiTest1.dir/test.cpp.o -MF CMakeFiles/smiTest1.dir/test.cpp.o.d -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/test.cpp -[ 53%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceField.dir/link.d CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Built target testMMFFForceField @@ -4689,13 +4720,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Reaction.cpp -[ 53%] Linking CXX executable graphmolTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 -[ 53%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTest1.dir/link.d CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../lib/libRDKitForceField.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 53%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolSGroupCatch.dir/link.d CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 53%] Built target graphmolTest1 +[ 53%] Built target graphmolSGroupCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" @@ -4704,11 +4733,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/catch_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Linking CXX executable graphmolAdjustQueryCatch -[ 53%] Built target graphmoltestChirality cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 +[ 53%] Linking CXX executable graphmoltestPickler +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolAdjustQueryCatch.dir/link.d CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 53%] Built target graphmolAdjustQueryCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake "--color=" @@ -4717,9 +4748,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolAdjustQueryCatch.dir/link.d CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 53%] Built target graphmolAdjustQueryCatch +[ 53%] Built target graphmoltestPickler make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" @@ -4728,11 +4759,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/testDepictor.cpp -[ 53%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestPickler.dir/link.d CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable molopsTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 53%] Built target graphmoltestPickler +[ 53%] Built target molopsTestsCatch make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake "--color=" @@ -4741,11 +4772,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/catch_tests.cpp -[ 53%] Linking CXX executable molopsTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molopsTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molopsTestsCatch.dir/link.d CMakeFiles/molopsTestsCatch.dir/catch_molops.cpp.o -o molopsTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable pickleTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickleTestsCatch.dir/link.d CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 53%] Built target molopsTestsCatch +[ 53%] Built target pickleTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" @@ -4767,11 +4798,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -MF CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o.d -o CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testAtropisomers.cpp -[ 53%] Linking CXX executable pickleTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/pickleTestsCatch.dir/link.d CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmoltestChirality.dir/link.d CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 53%] Built target pickleTestsCatch +[ 53%] Built target graphmoltestChirality make -f Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSquiggleDoubleBonds.dir/DependInfo.cmake "--color=" @@ -4795,11 +4826,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testMolSupplier.cpp -[ 53%] Linking CXX executable testAtropisomers -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable testSquiggleDoubleBonds +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSquiggleDoubleBonds.dir/link.d CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -o testSquiggleDoubleBonds ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 53%] Built target testAtropisomers +[ 53%] Built target testSquiggleDoubleBonds make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" @@ -4808,11 +4839,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testGeneralFileReader.cpp -[ 53%] Linking CXX executable testSquiggleDoubleBonds -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSquiggleDoubleBonds.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSquiggleDoubleBonds.dir/link.d CMakeFiles/testSquiggleDoubleBonds.dir/testSquiggleDoubleBonds.cpp.o -o testSquiggleDoubleBonds ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable testAtropisomers +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAtropisomers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAtropisomers.dir/link.d CMakeFiles/testAtropisomers.dir/testAtropisomers.cpp.o -o testAtropisomers ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 53%] Built target testSquiggleDoubleBonds +[ 53%] Built target testAtropisomers 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" @@ -4821,6 +4852,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp +[ 53%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ChemReactions/DaylightParser.cpp [ 54%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDepictor.dir/link.d CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4834,26 +4867,26 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testMolWriter.cpp -[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ChemReactions/DaylightParser.cpp -[ 54%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 54%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 55%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 54%] Built target testMultithreadedMolSupplier +[ 55%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o +[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testTpls.cpp -[ 55%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGeneralFileReader.dir/link.d CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 55%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMultithreadedMolSupplier.dir/link.d CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target testGeneralFileReader +[ 55%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" @@ -4862,13 +4895,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionPickler.cpp -[ 55%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target testTplParser +[ 55%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" @@ -4877,11 +4908,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testSequence.cpp -[ 55%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testTplParser.dir/link.d CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target testMol2ToMol +[ 55%] Built target testTplParser 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" @@ -4890,13 +4921,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -[ 55%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 -[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionWriter.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMol2ToMol.dir/link.d CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target depictorCatch +[ 55%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -4916,13 +4945,15 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/testPropertyLists.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolTestsCatch.dir/link.d CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionWriter.cpp +[ 55%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target graphmolTestsCatch +[ 55%] Built target chiralityTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" @@ -4931,11 +4962,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp -[ 55%] Linking CXX executable testMolSupplier -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +[ 55%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target testMolSupplier +[ 55%] Built target smiTest1 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" @@ -4944,11 +4975,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp -[ 55%] Linking CXX executable smiTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTestCatch.dir/link.d CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable depictorCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/depictorCatch.dir/link.d CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target smiTestCatch +[ 55%] Built target depictorCatch 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" @@ -4959,12 +4990,12 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp [ 55%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 +[ 55%] Linking CXX executable testMolSupplier +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testExtendedStereoParsing.dir/link.d CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Linking CXX executable testMolWriter [ 55%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' @@ -4972,9 +5003,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/connectTheDots_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolSupplier.dir/link.d CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target testMolWriter +[ 55%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/DependInfo.cmake "--color=" @@ -4983,13 +5014,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -MF CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o.d -o CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/v2_suppliers_catch.cpp -[ 55%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chiralityTestsCatch.dir/link.d CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolWriter.dir/link.d CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -[ 55%] Built target chiralityTestsCatch +[ 55%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -4998,9 +5027,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -MF CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o.d -o CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/v2_file_parsers_catch.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTest1.dir/link.d CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/smiTestCatch.dir/link.d CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target smiTest1 +[ 55%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/DependInfo.cmake "--color=" @@ -5011,11 +5042,11 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -MF CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o.d -o CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FileParsers/multithreaded_supplier_catch.cpp [ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionDepict.cpp -[ 55%] Linking CXX executable XYZFileParserCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable connectTheDotsTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target XYZFileParserCatchTest +[ 55%] Built target connectTheDotsTest make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" @@ -5024,21 +5055,21 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/test1.cpp -[ 55%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/connectTheDotsTest.dir/link.d CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable XYZFileParserCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/XYZFileParserCatchTest.dir/link.d CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 55%] Built target connectTheDotsTest +[ 55%] Built target XYZFileParserCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" -[ 55%] Linking CXX executable v2MolSuppliers make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Substruct/catch_tests.cpp +[ 55%] Linking CXX executable v2MolSuppliers +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2MolSuppliers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2MolSuppliers.dir/link.d CMakeFiles/v2MolSuppliers.dir/v2_suppliers_catch.cpp.o -o v2MolSuppliers ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Built target v2MolSuppliers @@ -5050,8 +5081,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 55%] Linking CXX executable v2FileParsersCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/v2FileParsersCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/v2FileParsersCatchTest.dir/link.d CMakeFiles/v2FileParsersCatchTest.dir/v2_file_parsers_catch.cpp.o -o v2FileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5064,7 +5093,9 @@ make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o +[ 55%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemTransforms/catch_tests.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp [ 56%] Linking CXX executable molfileStereoCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molfileStereoCatchTest.dir/link.d CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -5078,11 +5109,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp -[ 56%] Linking CXX executable multithreadedSupplierCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/multithreadedSupplierCatchTest.dir/link.d CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -o multithreadedSupplierCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 56%] Built target multithreadedSupplierCatchTest +[ 56%] Built target cdxmlParserCatchTest make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake "--color=" @@ -5091,13 +5122,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/test1.cpp -[ 56%] Linking CXX executable testPropertyLists -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPropertyLists.dir/link.d CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable multithreadedSupplierCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/multithreadedSupplierCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/multithreadedSupplierCatchTest.dir/link.d CMakeFiles/multithreadedSupplierCatchTest.dir/multithreaded_supplier_catch.cpp.o -o multithreadedSupplierCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 56%] Linking CXX executable cdxmlParserCatchTest -[ 56%] Built target testPropertyLists -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 +[ 56%] Built target multithreadedSupplierCatchTest make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" @@ -5106,9 +5135,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cdxmlParserCatchTest.dir/link.d CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable testPropertyLists +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPropertyLists.dir/link.d CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 56%] Built target cdxmlParserCatchTest +[ 56%] Built target testPropertyLists make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake "--color=" @@ -5134,10 +5165,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/test1.cpp -[ 57%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 [ 57%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/MoleculeParser.cpp +[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/BCUT.cpp +[ 57%] Linking CXX executable testFragCatalog +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFragCatalog.dir/link.d CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Built target testFragCatalog @@ -5149,13 +5182,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 57%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/BCUT.cpp -[ 57%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 57%] Built target testSubstructMatch +[ 57%] Built target graphmolMolOpsTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" @@ -5175,13 +5206,13 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 57%] Linking CXX executable testMHFPFingerprint -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 [ 57%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/catch_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSubstructMatch.dir/link.d CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 57%] Built target testMHFPFingerprint +[ 57%] Built target testSubstructMatch make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" @@ -5196,24 +5227,33 @@ | ^ [ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/ReactionRunner.cpp -[ 58%] Linking CXX executable chemTransformsTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chemTransformsTestCatch.dir/link.d CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 58%] Built target chemTransformsTestCatch +[ 58%] Built target fileParsersTest1 make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build -[ 58%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MolTransforms/test1.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemTransforms.dir/link.d CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMHFPFingerprint.dir/link.d CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 58%] Built target testChemTransforms +[ 58%] Built target testMHFPFingerprint +[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PreprocessRxn.cpp +[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp +[ 58%] Linking CXX executable chemTransformsTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chemTransformsTestCatch.dir/link.d CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 58%] Built target chemTransformsTestCatch make -f Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/DependInfo.cmake "--color=" @@ -5222,11 +5262,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/catch_tests.cpp -[ 58%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersTest1.dir/link.d CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable testChemTransforms +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testChemTransforms.dir/link.d CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 58%] Built target fileParsersTest1 +[ 58%] Built target testChemTransforms make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/DependInfo.cmake "--color=" @@ -5235,40 +5275,42 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/catch_tests.cpp -[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp +[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/SanitizeRxn.cpp +[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp [ 58%] Linking CXX executable molTransformsTestCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTransformsTestCatch.dir/link.txt --verbose=1 +[ 58%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTransformsTestCatch.dir/link.d CMakeFiles/molTransformsTestCatch.dir/catch_tests.cpp.o -o molTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Built target molTransformsTestCatch make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend +[ 58%] Built target testMolTransforms make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp -[ 58%] Linking CXX executable testMolTransforms -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -[ 58%] Linking CXX executable forceFieldHelpersCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolTransforms.dir/link.d CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 58%] Built target testMolTransforms -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 58%] Built target forceFieldHelpersCatch -make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend [ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp +[ 58%] Linking CXX executable fpGenTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 58%] Built target fpGenTestCatch +make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' @@ -5276,13 +5318,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -[ 58%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp -[ 58%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable forceFieldHelpersCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/forceFieldHelpersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/forceFieldHelpersCatch.dir/link.d CMakeFiles/forceFieldHelpersCatch.dir/catch_tests.cpp.o -o forceFieldHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 58%] Built target fileParsersCatchTest +[ 58%] Built target forceFieldHelpersCatch make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake "--color=" @@ -5291,11 +5331,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp -[ 58%] Linking CXX executable fpGenTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpGenTestCatch.dir/link.d CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpTestCatch.dir/link.d CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 58%] Built target fpGenTestCatch +[ 58%] Built target fpTestCatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" @@ -5306,13 +5346,15 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp [ 58%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolDescriptors.cpp -[ 58%] Linking CXX executable fpTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 -[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fpTestCatch.dir/link.d CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PNGParser.cpp +[ 58%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/CDXMLParser.cpp +[ 58%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/fileParsersCatchTest.dir/link.d CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 58%] Built target fpTestCatch +[ 58%] Built target fileParsersCatchTest make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" @@ -5323,40 +5365,40 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/catch_tests.cpp [ 59%] Linking CXX executable testMMFFForceFieldHelpersMultiThread cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -[ 59%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.d CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 59%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolSurf.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 59%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o +[ 60%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp -[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolSurf.cpp -[ 60%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -[ 60%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp +[ 60%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 60%] Built target testMMFFForceFieldHelpers +[ 60%] Built target testFingerprintGenerators make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build -[ 60%] Built target testCrystalForceField make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend [ 60%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testMolAlign.cpp +[ 60%] Linking CXX executable testCrystalForceField +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCrystalForceField.dir/link.d CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 60%] Built target testCrystalForceField +make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' @@ -5364,6 +5406,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/catch_tests.cpp +[ 60%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp +[ 60%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 60%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprints.dir/link.d CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -5377,11 +5423,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp -[ 60%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFingerprintGenerators.dir/link.d CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfragcatalog.dir/link.d -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.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 60%] Built target testFingerprintGenerators +[ 60%] Built target rdfragcatalog make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake "--color=" @@ -5390,13 +5436,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp -[ 60%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/SanitizeRxn.cpp -[ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdfragcatalog.dir/link.d -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.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 60%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMFFForceFieldHelpers.dir/link.d CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 60%] Built target rdfragcatalog +[ 60%] Built target testMMFFForceFieldHelpers 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake "--color=" @@ -5405,11 +5449,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/test1.cpp -[ 60%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceFieldHelpers.dir/link.d CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Lipinski.cpp +[ 60%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molAlignCatchTest.dir/link.d CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 60%] Built target testUFFForceFieldHelpers +[ 60%] Built target molAlignCatchTest make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake "--color=" @@ -5418,13 +5464,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/FMCS.cpp -[ 60%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 -[ 60%] Linking CXX executable molAlignCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testShapeHelpers.dir/link.d CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testUFFForceFieldHelpers.dir/link.d CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 60%] Built target testShapeHelpers +[ 60%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" @@ -5433,9 +5477,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MolHash/catch_tests.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molAlignCatchTest.dir/link.d CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 60%] Built target molAlignCatchTest +[ 60%] Built target testMolAlign make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake "--color=" @@ -5444,15 +5490,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/MMPA.cpp -[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Lipinski.cpp -[ 60%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 -[ 60%] Linking CXX executable testMolAlign -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp +[ 60%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testShapeHelpers.dir/link.d CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 60%] Built target testMolCatalog +[ 60%] Built target testShapeHelpers make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/DependInfo.cmake "--color=" @@ -5461,11 +5505,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalMCES.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolAlign.dir/link.d CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp +[ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 60%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/PNGParser.cpp -[ 60%] Built target testMolAlign +[ 60%] Built target rdDistGeom make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/DependInfo.cmake "--color=" @@ -5474,48 +5520,39 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.cpp -[ 61%] Linking CXX executable testFeatures -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFeatures.dir/link.d CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 60%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolCatalog.dir/link.d CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 61%] Built target testFeatures +[ 60%] Built target testMolCatalog make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o +[ 60%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Trajectory/trajectoryTest.cpp -[ 61%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDistGeom.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 61%] Built target rdDistGeom -[ 61%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o +[ 60%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpace.cpp -[ 61%] Linking CXX executable distGeomHelpersCatch +[ 60%] Linking CXX executable distGeomHelpersCatch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/distGeomHelpersCatch.dir/link.d CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 61%] Built target distGeomHelpersCatch +[ 60%] Built target distGeomHelpersCatch make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o +[ 60%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/External/rapidjson-1.1.0/include -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange/test1.cpp -[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -[ 61%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/CDXMLParser.cpp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp -[ 61%] Linking CXX executable trajectoryTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryTest.dir/link.d CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 61%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFeatures.dir/link.d CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 61%] Built target trajectoryTest +[ 61%] Built target testFeatures make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" @@ -5532,34 +5569,35 @@ 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake "--color=" -[ 61%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/catch_tests.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2024.09.6 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so +[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MQN.cpp +[ 62%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 61%] Built target MMPA +[ 62%] Built target ChemReactions make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o +[ 62%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolProcessing_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLPROCESSING_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -MF CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o.d -o CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/MolProcessing.cpp -[ 61%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +[ 62%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Seed.cpp -[ 61%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSet.cpp -[ 62%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molHashCatchTest.dir/link.d CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 62%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2024.09.6 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 62%] Built target molHashCatchTest +[ 62%] Built target MMPA make -f Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/build.make Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/DependInfo.cmake "--color=" @@ -5568,205 +5606,216 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/testMIF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInteractionFields/CMakeFiles/testMIF.dir/testMIF.cpp.o -MF CMakeFiles/testMIF.dir/testMIF.cpp.o.d -o CMakeFiles/testMIF.dir/testMIF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/testMIF.cpp -[ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MQN.cpp -[ 62%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeTest1.dir/link.d CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 62%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSet.cpp +[ 63%] Linking CXX executable molHashCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molHashCatchTest.dir/link.d CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 62%] Built target molInterchangeTest1 -make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend +[ 63%] Built target molHashCatchTest +make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build +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-202409.6/obj-aarch64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MMPA/MMPA_UnitTest.cpp -[ 62%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -fpermissive -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp -[ 63%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp +[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/Property.cpp +[ 63%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.cpp +[ 63%] Linking CXX executable trajectoryTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/trajectoryTest.dir/link.d CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 63%] Built target trajectoryTest +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 63%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/ChemReactions/testReaction.cpp [ 63%] Linking CXX shared library ../../../lib/libRDKitMolProcessing.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolProcessing.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolProcessing.so.1 -o ../../../lib/libRDKitMolProcessing.so.1.2024.09.6 CMakeFiles/MolProcessing.dir/MolProcessing.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../lib/libRDKitMolProcessing.so.1 ../../../lib/libRDKitMolProcessing.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 63%] Built target MolProcessing -make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/Property.cpp -[ 63%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Synthon.cpp -[ 63%] Linking CXX executable molInterchangeCatchTest +[ 63%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp +[ 64%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp +[ 64%] Linking CXX executable molInterchangeTest1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeTest1.dir/link.d CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 64%] Built target molInterchangeTest1 +[ 64%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinWriter.cpp +[ 64%] Linking CXX executable molInterchangeCatchTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molInterchangeCatchTest.dir/link.d CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 63%] Built target molInterchangeCatchTest -make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/depend +[ 64%] Built target molInterchangeCatchTest +make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend +[ 64%] Linking CXX executable testAbbreviations +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build +make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -MF CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o.d -o CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/processing_tests.cpp -[ 63%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalCluster.cpp -[ 63%] Linking CXX executable testAbbreviations -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 +[ 64%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp +[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AUTOCORR2D.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAbbreviations.dir/link.d CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 63%] Built target testAbbreviations -make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend +[ 64%] Built target testAbbreviations +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolProcessing_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -MF CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o.d -o CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp -[ 63%] Linking CXX executable testMIF +[ 64%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/catch_tests.cpp +[ 64%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Synthon.cpp +[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalCluster.cpp +[ 64%] Linking CXX executable testMIF cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMIF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMIF.dir/link.d CMakeFiles/testMIF.dir/testMIF.cpp.o -o testMIF ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInteractionFields.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 63%] Built target testMIF -[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp -[ 64%] Linking CXX executable testMMPA -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 64%] Built target testMIF +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 64%] Built target testMMPA -[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp -[ 64%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 64%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/MolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.cpp +[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp +[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp +[ 64%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReactionFingerprints.dir/link.d CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 64%] Built target rdMMPA -[ 64%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.cpp -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AUTOCORR2D.cpp -[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -MF CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.cpp +[ 64%] Built target testReactionFingerprints +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 64%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp +[ 64%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.cpp [ 64%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSearcher.cpp -[ 64%] Linking CXX executable testMolProcessing -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolProcessing.dir/link.d CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -o testMolProcessing ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolProcessing.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 64%] Built target testMolProcessing -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp [ 64%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceSubstructureSearcher.cpp -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp -[ 64%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalResult.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.cpp [ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/USRDescriptor.cpp -[ 64%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o +[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp +[ 65%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 65%] Built target testEnumeration +make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 65%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +[ 65%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/SubstructMatchCustom.cpp +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/bits/stl_tree.h:63, + from /usr/include/c++/14/map:62, + from /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Dict.h:19, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:16, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:16: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:768:42: required from here + 768 | auto new_mins = getAtomCoords(make_pair(x_min, y_min)); + | ~~~~~~~~~^~~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/RascalMCES/lap_a_la_scipy.cpp +[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -MF CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o.d -o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/PartitionSet.cpp +[ 65%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalResult.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/RascalResult.cpp +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AtomFeat.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/OxidationNumbers.cpp.o -MF CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o.d -o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/OxidationNumbers.cpp -[ 65%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp -[ 65%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.cpp.o +[ 66%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SYNTHONSPACESEARCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -MF CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o.d -o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/SynthonSpaceFingerprintSearcher.cpp +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DCLV.cpp.o -MF CMakeFiles/Descriptors.dir/DCLV.cpp.o.d -o CMakeFiles/Descriptors.dir/DCLV.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/DCLV.cpp +[ 66%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/FMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 65%] Built target FMCS -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/testFMCS_Unit.cpp -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend +[ 66%] Built target FMCS +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-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp -[ 65%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolProcessing.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolProcessing.so CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o ../../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDStreams.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 66%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp +[ 66%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/MolStandardize.cpp +[ 66%] Linking CXX executable testMMPA +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMMPA.dir/link.d CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 65%] Built target rdMolProcessing -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend +[ 66%] Built target testMMPA +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Test/testFMCS.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o +[ 67%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.cpp +[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/EEM.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/PBF.cpp -[ 65%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp -[ 65%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/PMI.cpp +[ 67%] Linking CXX shared library ../../../lib/libRDKitSynthonSpaceSearch.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/SynthonSpaceSearch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSynthonSpaceSearch.so.1 -o ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearch_details.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpace.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSet.cpp.o CMakeFiles/SynthonSpaceSearch.dir/Synthon.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceSubstructureSearcher.cpp.o CMakeFiles/SynthonSpaceSearch.dir/SynthonSpaceFingerprintSearcher.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1 ../../../lib/libRDKitSynthonSpaceSearch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 65%] Built target SynthonSpaceSearch -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AUTOCORR3D.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RDF.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/GETAWAY.cpp -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/WHIM.cpp -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/CoulombMat.cpp -[ 67%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 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.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 67%] Built target ChemReactions -make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -MF CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o.d -o CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Wrap/rdSynthonSpaceSearch.cpp -[ 67%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 -[ 67%] Linking CXX executable FMCStest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/graphmolMolOpsTest.dir/link.d CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../lib/libRDKitAlignment.so.1.2024.09.6 ../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 67%] Built target graphmolMolOpsTest +[ 67%] Built target SynthonSpaceSearch make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake "--color=" @@ -5775,159 +5824,126 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Deprotect.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/FMCStest.dir/link.d CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMMPA.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 67%] Built target FMCStest +[ 67%] Built target rdMMPA make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 67%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 [ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdmolops.cpp -make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' +[ 67%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/PositionVariation.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/AUTOCORR3D.cpp +[ 67%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Metal.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/RDF.cpp +[ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolOps.cpp +[ 67%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/MORSE.cpp +[ 67%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 +[ 67%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRascalMCES.so.1 -o ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o CMakeFiles/RascalMCES.dir/PartitionSet.cpp.o CMakeFiles/RascalMCES.dir/RascalResult.cpp.o ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so -[ 67%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinParser.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 67%] Built target RascalMCES -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend +make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build +make -f Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build.make Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/ChemReactions/testReaction.cpp -[ 67%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinWriter.cpp -[ 67%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/MarvinDefs.cpp -[ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolOps.cpp -[ 67%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/ChiralityOps.cpp -[ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -[ 68%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 -[ 68%] Linking CXX executable testFMCS -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 +[ 67%] Building CXX object Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolProcessing/CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -MF CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o.d -o CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/processing_tests.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Deprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2024.09.6 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2024.09.6 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 68%] Built target Deprotect -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend -[ 68%] Built target rdFMCS -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build +[ 67%] Built target Deprotect +make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build -[ 68%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o +make -f Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build.make Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp -[ 68%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFMCS.dir/link.d CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 67%] Building CXX object Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolProcessing_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolProcessing/Wrap/CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -MF CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o.d -o CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/rdMolProcessing.cpp +[ 67%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 68%] Built target testFMCS -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +[ 67%] Built target MarvinParser +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/catch_tests.cpp -[ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 67%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/testFMCS_Unit.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/GETAWAY.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/WHIM.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Descriptors/CoulombMat.cpp +[ 69%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp +[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Normalize.cpp +[ 69%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/LinkNode.cpp +[ 69%] Linking CXX executable testMolProcessing +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolProcessing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolProcessing.dir/link.d CMakeFiles/testMolProcessing.dir/processing_tests.cpp.o -o testMolProcessing ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolProcessing.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDStreams.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 68%] Built target rdSynthonSpaceSearch -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend +[ 69%] Built target testMolProcessing +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-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build +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-202409.6/obj-aarch64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/MolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/MolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Pipeline.cpp -[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/MolStandardize.cpp -[ 68%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Metal.cpp -[ 68%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReactionFingerprints.dir/link.d CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 68%] Built target testReactionFingerprints -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend +[ 69%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp +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-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp -[ 68%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp -[ 68%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEnumeration.dir/link.d CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 69%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Test/testFMCS.cpp +[ 69%] Linking CXX executable rxnTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rxnTestCatch.dir/link.d CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 68%] Built target testEnumeration +[ 69%] Built target rxnTestCatch make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 69%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o +[ 70%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/mces_catch.cpp -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/bits/stl_tree.h:63, - from /usr/include/c++/14/map:62, - from /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Dict.h:19, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/QueryOps.h:16, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:16: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:768:42: required from here - 768 | auto new_mins = getAtomCoords(make_pair(x_min, y_min)); - | ~~~~~~~~~^~~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Normalize.cpp -[ 69%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Validate.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Descriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2024.09.6 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/DCLV.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.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so -[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdMolProcessing.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolProcessing.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolProcessing.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolProcessing.so CMakeFiles/rdMolProcessing.dir/rdMolProcessing.cpp.o ../../../../lib/libRDKitMolProcessing.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDStreams.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 70%] Built target Descriptors +[ 70%] Built target rdMolProcessing make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/DependInfo.cmake "--color=" @@ -5936,12 +5952,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp -[ 70%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MarvinParser.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so +[ 70%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Validate.cpp +[ 70%] Linking CXX executable FMCStest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/FMCStest.dir/link.d CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 70%] Built target MarvinParser +[ 70%] Built target FMCStest make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/DependInfo.cmake "--color=" @@ -5950,662 +5967,276 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 70%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp -[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp -[ 71%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 71%] Linking CXX executable testRascalCluster +[ 70%] Linking CXX executable testRascalCluster cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalCluster.dir/link.d CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 71%] Built target testRascalCluster -make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend +[ 70%] Built target testRascalCluster +make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build +make -f Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/MolEnumerator.cpp -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Fragment.cpp -[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +[ 70%] Building CXX object Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSynthonSpaceSearch_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SynthonSpaceSearch/Wrap/CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -MF CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o.d -o CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/Wrap/rdSynthonSpaceSearch.cpp +[ 70%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/AtomSymbol.cpp -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp -[ 72%] Linking CXX executable testRascalMCES -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalMCES.dir/link.d CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 70%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +[ 70%] Linking CXX executable testFMCS +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testFMCS.dir/link.d CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 72%] Built target testRascalMCES +[ 70%] Built target testFMCS make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o +[ 70%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/catch_tests.cpp.o -MF CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/catch_tests.cpp -[ 72%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolops.dir/link.d -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.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 72%] Built target rdmolops -[ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPMol.cpp -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp -[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 70%] Linking CXX executable testRascalMCES +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRascalMCES.dir/link.d CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 72%] Built target rdRascalMCES +[ 70%] Built target testRascalMCES make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o +[ 70%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/deprotectTest.cpp -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp -[ 72%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/PositionVariation.cpp -[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp -[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp -[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.cpp -[ 73%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp -[ 73%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 -[ 73%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rxnTestCatch.dir/link.d CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdFMCS.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 73%] Built target rxnTestCatch +[ 71%] Built target rdFMCS make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 73%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o +[ 71%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp -[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp -[ 74%] Linking CXX executable deprotectTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/deprotectTest.dir/link.d CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDeprotect.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 72%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Charge.cpp +[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRascalMCES.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 74%] Built target deprotectTest +[ 72%] Built target rdRascalMCES make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o +[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdchem.cpp.o -MF CMakeFiles/rdchem.dir/rdchem.cpp.o.d -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdchem.cpp -[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp -[ 74%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +[ 72%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp -[ 74%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Digraph.cpp -[ 74%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/LinkNode.cpp -[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Node.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Edge.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Sort.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/AtropisomerBond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp -[ 74%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 75%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 CMakeFiles/MolStandardize.dir/Pipeline.cpp.o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so -[ 75%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Table.cpp +[ 72%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdSynthonSpaceSearch.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSynthonSpaceSearch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSynthonSpaceSearch.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSynthonSpaceSearch.so CMakeFiles/rdSynthonSpaceSearch.dir/rdSynthonSpaceSearch.cpp.o ../../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 75%] Built target MolStandardize +[ 72%] Built target rdSynthonSpaceSearch make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o +[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/rdmolfiles.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 75%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDeprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 75%] Built target rdDeprotect -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/test1.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule6.cpp -[ 76%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 76%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testNormalize.cpp -[ 76%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testValidate.cpp -In file included from /usr/include/c++/14/vector:62, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: -In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', - inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, - inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, - inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, - inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, - inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: -/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] - 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, - from /usr/include/c++/14/bits/allocator.h:46, - from /usr/include/c++/14/vector:63: -In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', - inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, - inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, - inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: -/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' - 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); - | ^ -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 76%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MolStandardize/testCharge.cpp -[ 76%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -[ 76%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawShape.cpp -[ 76%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Table.cpp -[ 76%] Linking CXX executable testCIPLabeler -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCIPLabeler.dir/link.d CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 76%] Built target testCIPLabeler -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 76%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testTautomer.cpp -[ 76%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp -[ 76%] Linking CXX executable molNormalizeTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molNormalizeTest.dir/link.d CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 76%] Built target molNormalizeTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 76%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/test2.cpp -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/string:51, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.h:19, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp:13: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp:165:47: required from here - 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.y)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 76%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp -[ 76%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +[ 72%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMol.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 76%] Built target MolEnumerator -[ 77%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp -[ 78%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molValidateTest.dir/link.d CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Built target molValidateTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MolStandardize/testFragment.cpp -[ 78%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Built target molChargeTest -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-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/catch_tests.cpp -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp -[ 78%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextJS.cpp -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Built target molStandardizeTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/molStandardizePipelineTest.dir/testPipeline.cpp.o -MF CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o.d -o CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testPipeline.cpp -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MaeMolSupplier.cpp -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Atom.cpp -[ 78%] Linking CXX executable molStandardizeSmallTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Built target molStandardizeSmallTest -make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFT.cpp -[ 78%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReaction.dir/link.d CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Built target testReaction -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp -[ 78%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp -[ 78%] Linking CXX executable molFragmentTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molFragmentTest.dir/link.d CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Built target molFragmentTest -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/enumerator_catch.cpp -[ 78%] Linking CXX executable molTautomerTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTautomerTest.dir/link.d CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 78%] Built target molTautomerTest +[ 72%] Built target MolEnumerator make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 79%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o +[ 73%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SmilesParse/cxsmiles_test.cpp -[ 79%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Validate.cpp -[ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MaeWriter.cpp -[ 80%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so +[ 73%] Linking CXX executable deprotectTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/deprotectTest.dir/link.d CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDeprotect.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 80%] Built target MolDraw2D +[ 73%] Built target deprotectTest 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o +[ 74%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -MF CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o.d -o CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MarvinParse/testMrvToMol.cpp -[ 81%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +[ 74%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/Descriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2024.09.6 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/DCLV.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.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 81%] Built target ScaffoldNetwork +[ 74%] Built target Descriptors make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o +[ 74%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -MF CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o.d -o CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GenericGroups/generic_tests.cpp -[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SDMolSupplier.cpp -[ 81%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Charge.cpp -[ 82%] Linking CXX executable molStandardizePipelineTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizePipelineTest.dir/link.d CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -o molStandardizePipelineTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/ChiralityOps.cpp +[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPMol.cpp +[ 74%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Atom.cpp +[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/CIPLabeler.cpp +[ 75%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdDeprotect.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 82%] Built target molStandardizePipelineTest +[ 75%] Built target rdDeprotect make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' 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-202409.6/obj-aarch64-linux-gnu' -[ 82%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o +[ 75%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp -[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/TDTMolSupplier.cpp -[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/Bond.cpp -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 -[ 83%] Linking CXX executable molStandardizeCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 83%] Built target rdMolEnumerator -make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 84%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_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 -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/TautomerQuery.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeCatchTest.dir/link.d CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 75%] Linking CXX executable testReaction +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testReaction.dir/link.d CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 84%] Built target molStandardizeCatchTest +[ 75%] Built target testReaction 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 84%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/test.cpp -[ 85%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SmilesMolSupplier.cpp -[ 85%] Linking CXX executable testMrvToMol +[ 75%] Linking CXX executable testMrvToMol cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMrvToMol.dir/link.d CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 85%] Built target testMrvToMol +[ 75%] Built target testMrvToMol make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 85%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp -[ 86%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 75%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 +[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 75%] Linking CXX executable testGenericGroups +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolops.dir/link.d -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.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 86%] Built target testMolEnumerator +[ 75%] Built target rdmolops make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 86%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testATF.cpp -[ 86%] Linking CXX executable testGenericGroups -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGenericGroups.dir/link.d CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 86%] Built target testGenericGroups +[ 75%] Built target testGenericGroups make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 86%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o -MF CMakeFiles/testBCUT.dir/testBCUT.cpp.o.d -o CMakeFiles/testBCUT.dir/testBCUT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testBCUT.cpp -[ 86%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp -[ 86%] Linking CXX executable cxsmilesTest +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/Bond.cpp +[ 75%] Linking CXX executable cxsmilesTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/cxsmilesTest.dir/link.d CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 86%] Built target cxsmilesTest +[ 75%] Built target cxsmilesTest make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 86%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testEEM.cpp -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SmilesWriter.cpp -[ 86%] Linking CXX executable testAUTOCORR2D -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAUTOCORR2D.dir/link.d CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 75%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Fragment.cpp +[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 75%] Linking CXX executable testATF +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testATF.dir/link.d CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 86%] Built target testAUTOCORR2D +[ 75%] Built target testATF make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 87%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o +[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o -MF CMakeFiles/testPBF.dir/testPBF.cpp.o.d -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testPBF.cpp -[ 87%] Linking CXX executable testATF -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testATF.dir/link.d CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 76%] Linking CXX executable testAUTOCORR2D +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAUTOCORR2D.dir/link.d CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 87%] Built target testATF +[ 76%] Built target testAUTOCORR2D make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 87%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -[ 88%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o +[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -MF CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o.d -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testRDFcustom.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +[ 77%] Linking CXX executable testBCUT +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testBCUT.dir/link.d CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 88%] Built target TautomerQuery +[ 77%] Built target testBCUT make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 88%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o +[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o -MF CMakeFiles/testRDF.dir/testRDF.cpp.o.d -o CMakeFiles/testRDF.dir/testRDF.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testRDF.cpp -[ 88%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Metal.cpp -[ 88%] Linking CXX executable testBCUT -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testBCUT.dir/link.d CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 88%] Built target testBCUT -make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 88%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testMORSE.cpp -[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SDWriter.cpp -[ 88%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp -[ 89%] Linking CXX executable testEEM -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEEM.dir/link.d CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 89%] Built target testEEM -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 90%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -MF CMakeFiles/test3D.dir/test3D.cpp.o.d -o CMakeFiles/test3D.dir/test3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/test3D.cpp -[ 90%] Linking CXX executable testRDF -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDF.dir/link.d CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 90%] Built target testRDF -make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/depend -[ 90%] Linking CXX executable testRDFcustom -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o -MF CMakeFiles/testWHIM.dir/testWHIM.cpp.o.d -o CMakeFiles/testWHIM.dir/testWHIM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testWHIM.cpp -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Mol.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDFcustom.dir/link.d CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target testRDFcustom -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-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -MF CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o.d -o CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testGETAWAY.cpp +[ 77%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Node.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, @@ -6653,124 +6284,415 @@ /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/TDTWriter.cpp -[ 91%] Linking CXX executable testPBF +[ 77%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp +[ 78%] Linking CXX executable testEEM +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Mol.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testEEM.dir/link.d CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 78%] Built target testEEM +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testMORSE.cpp +[ 78%] Linking CXX executable testPBF cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 +[ 78%] Linking CXX executable testRDF +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testPBF.dir/link.d CMakeFiles/testPBF.dir/testPBF.cpp.o -o testPBF ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target testPBF +[ 78%] Built target testPBF +make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -MF CMakeFiles/test3D.dir/test3D.cpp.o.d -o CMakeFiles/test3D.dir/test3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/test3D.cpp +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDF.dir/link.d CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 79%] Built target testRDF +make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o -MF CMakeFiles/testWHIM.dir/testWHIM.cpp.o.d -o CMakeFiles/testWHIM.dir/testWHIM.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testWHIM.cpp +[ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +[ 80%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Edge.cpp +[ 80%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp +[ 80%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Sort.cpp +[ 80%] Linking CXX executable testRDFcustom +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRDFcustom.dir/link.d CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 80%] Built target testRDFcustom +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-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -MF CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o.d -o CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testGETAWAY.cpp +[ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp +[ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 80%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Conformer.cpp +[ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 81%] Linking CXX executable testMORSE +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMORSE.dir/link.d CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 81%] Built target testMORSE make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -MF CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o.d -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp -[ 91%] Linking CXX executable testMORSE -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMORSE.dir/link.d CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 81%] Linking CXX executable testDescriptors +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDescriptors.dir/link.d CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target testMORSE +[ 81%] Built target testDescriptors make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -MF CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o.d -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/testCoulombMat.cpp -[ 91%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp -[ 91%] Linking CXX executable testDescriptors -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testDescriptors.dir/link.d CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 81%] Linking CXX executable testWHIM +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testWHIM.dir/link.d CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target testDescriptors +[ 81%] Built target testWHIM make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/catch_tests.cpp -[ 91%] Linking CXX executable testGETAWAY +[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 81%] Linking CXX executable testGETAWAY cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testGETAWAY.dir/link.d CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target testGETAWAY +[ 81%] Built target testGETAWAY make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake "--color=" -[ 91%] Linking CXX executable testWHIM -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o +[ 81%] Building CXX object Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDescriptors_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -MF CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o.d -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/PDBWriter.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testWHIM.dir/link.d CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp +[ 81%] Linking CXX executable test3D +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test3D.dir/link.d CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target testWHIM +[ 81%] Built target test3D make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +[ 81%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp -[ 91%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 -[ 91%] Linking CXX executable testAUTOCORR3D +[ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp +[ 81%] Linking CXX executable testAUTOCORR3D cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAUTOCORR3D.dir/link.d CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 81%] Built target testAUTOCORR3D +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 81%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 81%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCoulombMat.dir/link.d CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target testCoulombMat +[ 81%] Built target testCoulombMat +make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend +[ 81%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MaeMolSupplier.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 81%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp +/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': +/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:444:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 444 | python::list atomprops) { + | ^ +[ 81%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/AtropisomerBond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/configs/AtropisomerBond.cpp +[ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp +In file included from /usr/include/c++/14/vector:62, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: +In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', + inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:521:30, + inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:548:42, + inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:555:31, + inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = int*]' at /usr/include/c++/14/bits/stl_algobase.h:651:7, + inlined from 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:147:27, + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*]' at /usr/include/c++/14/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = int*; _Tp = int]' at /usr/include/c++/14/bits/stl_uninitialized.h:373:37, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1022:38, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: +/usr/include/c++/14/bits/stl_algobase.h:452:30: warning: 'void* __builtin_memmove(void*, const void*, long unsigned int)' writing between 5 and 9223372036854775804 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] + 452 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, + from /usr/include/c++/14/bits/allocator.h:46, + from /usr/include/c++/14/vector:63: +In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', + inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, + inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:1013:40, + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:1488:19, + inlined from 'void RDKit::MolDraw2D_detail::DrawMolMCHLasso::extractAtomColourLists(std::vector&, std::vector >&, std::vector >&) const' at /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:115:32: +/usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' + 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); + | ^ +[ 81%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 81%] Built target descriptorsTestCatch +[ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawShape.cpp +[ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp +[ 81%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp +[ 82%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/RingInfo.cpp +[ 83%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 83%] Built target O3AAlign +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 83%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp +[ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/string:51, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.h:19, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp:13: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawText.cpp:165:47: required from here + 165 | tl = mol_draw.getAtomCoords(std::make_pair(tl.x, tl.y)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 83%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MaeWriter.cpp +[ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp +[ 85%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolEnumerator.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 85%] Built target rdMolEnumerator +make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 85%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +In file included from /usr/include/c++/14/bits/stl_algobase.h:64, + from /usr/include/c++/14/string:51, + from /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Invariant.h:17, + from /build/reproducible-path/rdkit-202409.6/Code/Numerics/Matrix.h:14, + from /build/reproducible-path/rdkit-202409.6/Code/Numerics/SquareMatrix.h:14, + from /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform3D.h:16, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: +/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here + 643 | oscores.push_back(std::make_pair(rmsd, score)); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ +/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1132 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextJS.cpp +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp +[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/EditableMol.cpp +[ 86%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MonomerInfo.cpp +[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +[ 87%] Linking CXX executable testMolEnumerator +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testMolEnumerator.dir/link.d CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 87%] Built target testMolEnumerator +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp +[ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 87%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SDMolSupplier.cpp +[ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 87%] Linking CXX executable testO3AAlign +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testO3AAlign.dir/link.d CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 87%] Built target testO3AAlign +[ 87%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFT.cpp +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp +[ 88%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +[ 89%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp +[ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 89%] Built target rdChemReactions +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/TDTMolSupplier.cpp +[ 89%] Linking CXX executable testCIPLabeler +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testCIPLabeler.dir/link.d CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/configs/AtropisomerBond.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 89%] Built target testCIPLabeler +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolBundle.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/StereoGroup.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SubstanceGroup.cpp +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp +[ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 89%] Built target rdMolAlign +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Chirality.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SmilesMolSupplier.cpp +[ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDescriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 89%] Built target rdMolDescriptors +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SmilesWriter.cpp +[ 89%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 89%] Built target MolDraw2D make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/test1.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testAUTOCORR3D.dir/link.d CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target testAUTOCORR3D make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/catch_tests.cpp -[ 91%] Linking CXX executable test3D -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/test3D.dir/link.d CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Built target test3D -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/rxn_test1.cpp -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:444:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 444 | python::list atomprops) { - | ^ In file included from /usr/include/c++/14/bits/stl_algobase.h:64, from /usr/include/c++/14/bits/specfun.h:43, from /usr/include/c++/14/cmath:3906, @@ -6784,199 +6706,321 @@ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp -In file included from /usr/include/boost/python/override.hpp:13, - from /usr/include/boost/python/wrapper.hpp:8, - from /usr/include/boost/python/object/value_holder.hpp:15, - from /usr/include/boost/python/object/class_metadata.hpp:14, - from /usr/include/boost/python/class.hpp:23, - from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, - from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', - inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: -/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | ); - | ^ -In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12: -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: note: '' declared here - 617 | long to = extract( slice->stop); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', - inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: -/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | ); - | ^ -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': -/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: note: '' declared here - 603 | long from = extract( slice->start); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/rxn_test1.cpp make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SDWriter.cpp +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp -[ 92%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/descriptorsTestCatch.dir/link.d CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/TDTWriter.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/PDBWriter.cpp +[ 89%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/MolStandardize.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 CMakeFiles/MolStandardize.dir/Pipeline.cpp.o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 92%] Built target descriptorsTestCatch -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend +[ 89%] Built target MolStandardize +make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build +make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend -[ 92%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 +[ 90%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_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 -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/TautomerQuery.cpp +[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp +[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/test1.cpp +[ 91%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DRxnTest1.dir/link.d CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 92%] Built target moldraw2DRxnTest1 -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend +[ 91%] Built target moldraw2DRxnTest1 +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp -[ 93%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/O3AAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testNormalize.cpp +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 93%] Built target O3AAlign -make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testValidate.cpp +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build +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-202409.6/obj-aarch64-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -[ 93%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolStandardize.dir/link.d -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 CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MolStandardize/testCharge.cpp +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testTautomer.cpp +[ 91%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/TautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Built target TautomerQuery +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/test2.cpp +[ 91%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 +make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 93%] Built target rdMolStandardize +make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MolStandardize/testFragment.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdchem.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Built target rdchem +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-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/catch_tests.cpp +[ 91%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolfiles.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Built target rdmolfiles +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/molStandardizePipelineTest.dir/testPipeline.cpp.o -MF CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o.d -o CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/testPipeline.cpp +[ 91%] Linking CXX executable molNormalizeTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molNormalizeTest.dir/link.d CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Built target molNormalizeTest +make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp +[ 91%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeTest.dir/link.d CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Built target molStandardizeTest +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 91%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -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-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp +[ 92%] Linking CXX executable molValidateTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molValidateTest.dir/link.d CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 92%] Linking CXX executable molChargeTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 +[ 92%] Built target molValidateTest 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o +[ 92%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/catch_tests.cpp -[ 93%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdmolfiles.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molChargeTest.dir/link.d CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 93%] Built target rdmolfiles +[ 92%] Built target molChargeTest 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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +[ 92%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp -[ 93%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp -[ 93%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 92%] Linking CXX executable molStandardizeSmallTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeSmallTest.dir/link.d CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 93%] Built target tautomerQueryTestCatch -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend +[ 92%] Built target molStandardizeSmallTest +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp -[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp -[ 94%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp +[ 92%] Linking CXX executable molFragmentTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molFragmentTest.dir/link.d CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 94%] Built target rdScaffoldNetwork -make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend +[ 92%] Built target molFragmentTest +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 94%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Conformer.cpp -In file included from /usr/include/c++/14/bits/stl_algobase.h:64, - from /usr/include/c++/14/string:51, - from /build/reproducible-path/rdkit-202409.6/Code/RDGeneral/Invariant.h:17, - from /build/reproducible-path/rdkit-202409.6/Code/Numerics/Matrix.h:14, - from /build/reproducible-path/rdkit-202409.6/Code/Numerics/SquareMatrix.h:14, - from /build/reproducible-path/rdkit-202409.6/Code/Geometry/Transform3D.h:16, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/AlignMolecules.h:14, - from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: -/usr/include/c++/14/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here - 643 | oscores.push_back(std::make_pair(rmsd, score)); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~ -/usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1132 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 95%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +[ 92%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp +[ 92%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 92%] Built target moldraw2DTest1 +[ 92%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Validate.cpp +[ 92%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/ScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 92%] Built target ScaffoldNetwork +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp +[ 92%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp +[ 92%] Linking CXX executable molTautomerTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molTautomerTest.dir/link.d CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 92%] Built target molTautomerTest +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp +[ 92%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tautomerQueryTestCatch.dir/link.d CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 92%] Built target tautomerQueryTestCatch +[ 92%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Charge.cpp +[ 93%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp +[ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdTautomerQuery.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 95%] Built target rdTautomerQuery -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupData.cpp -[ 96%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 -[ 96%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 -[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testScaffoldNetwork.dir/link.d CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 93%] Built target rdTautomerQuery +[ 93%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +[ 94%] Linking CXX executable molStandardizePipelineTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizePipelineTest.dir/link.txt --verbose=1 +[ 94%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizePipelineTest.dir/link.d CMakeFiles/molStandardizePipelineTest.dir/testPipeline.cpp.o -o molStandardizePipelineTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target testScaffoldNetwork -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +[ 94%] Built target molStandardizePipelineTest +[ 94%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Metal.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 94%] Built target rdMolDraw2D +[ 94%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp +[ 94%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/molStandardizeCatchTest.dir/link.d CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 94%] Built target molStandardizeCatchTest +[ 94%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp +[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupData.cpp +[ 95%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Pipeline.cpp +[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp +[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp +[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp +[ 95%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 +[ 95%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/GeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target GeneralizedSubstruct +[ 95%] Built target GeneralizedSubstruct make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o +[ 95%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdChemReactions.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdScaffoldNetwork.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target rdChemReactions +[ 96%] Built target rdScaffoldNetwork make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" @@ -6985,11 +7029,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp -[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDescriptors.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 96%] Linking CXX executable testScaffoldNetwork +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testScaffoldNetwork.dir/link.d CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target rdMolDescriptors +[ 96%] Built target testScaffoldNetwork make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" @@ -6998,11 +7042,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp -[ 96%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTest1.dir/link.d CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target moldraw2DTest1 +[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp +[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp make -f Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/build.make Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/DependInfo.cmake "--color=" @@ -7011,59 +7054,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 96%] Building CXX object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/adapter.cpp.o -MF CMakeFiles/rdkit.dir/adapter.cpp.o.d -o CMakeFiles/rdkit.dir/adapter.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp -[ 96%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testO3AAlign.dir/link.d CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitDistGeomHelpers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitDistGeometry.so.1.2024.09.6 ../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target testO3AAlign [ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/PatternFactory.cpp -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp -/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': -/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:38: warning: unused parameter 'data' [-Wunused-parameter] - 1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, - | ~~~~~~~^~~~ -/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:49: warning: unused parameter 'isQuery' [-Wunused-parameter] - 1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, - | ~~~~~^~~~~~~ -/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1628:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] - 1628 | unsigned int bitFlags) { - | ~~~~~~~~~~~~~^~~~~~~~ -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/RingInfo.cpp -[ 96%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target rdGeneralizedSubstruct -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolDraw2D.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/EditableMol.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target rdMolDraw2D -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MonomerInfo.cpp -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp -[ 96%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp -[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolAlign.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitForceFieldHelpers.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitForceField.so.1.2024.09.6 ../../../../lib/libRDKitOptimizer.so.1.2024.09.6 ../../../../lib/libRDKitTrajectory.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target rdMolAlign -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp -[ 96%] Linking CXX executable generalizedSubstructCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/generalizedSubstructCatch.dir/link.d CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 96%] Built target generalizedSubstructCatch [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/bfp_op.c.o -MF CMakeFiles/rdkit.dir/bfp_op.c.o.d -o CMakeFiles/rdkit.dir/bfp_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/bfp_op.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/cache.c.o @@ -7072,6 +7064,35 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/guc.c.o -MF CMakeFiles/rdkit.dir/guc.c.o.d -o CMakeFiles/rdkit.dir/guc.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/guc.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/low_gist.c.o -MF CMakeFiles/rdkit.dir/low_gist.c.o.d -o CMakeFiles/rdkit.dir/low_gist.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/low_gist.c +In file included from /usr/include/boost/python/override.hpp:13, + from /usr/include/boost/python/wrapper.hpp:8, + from /usr/include/boost/python/object/value_holder.hpp:15, + from /usr/include/boost/python/object/class_metadata.hpp:14, + from /usr/include/boost/python/class.hpp:23, + from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, + from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, + from /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', + inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: +/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | ); + | ^ +In file included from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12: +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:617:27: note: '' declared here + 617 | long to = extract( slice->stop); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = long int]', + inlined from 'boost::python::extract::operator result_type() const [with T = long int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: +/usr/include/boost/python/extract.hpp:185:11: warning: '*(long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | ); + | ^ +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp: In static member function 'static void boost::python::detail::slice_helper::base_get_slice_data(Container&, PySliceObject*, Index&, Index&) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, long unsigned int, boost::python::detail::final_vector_derived_policies, false> >, long unsigned int>; Data = RDKit::MolStandardize::TautomerScoringFunctions::SubstructTerm; Index = long unsigned int]': +/usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:603:29: note: '' declared here + 603 | long from = extract( slice->start); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/mol_op.c.o -MF CMakeFiles/rdkit.dir/mol_op.c.o.d -o CMakeFiles/rdkit.dir/mol_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/mol_op.c [ 96%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rdkit_gist.c.o @@ -7088,24 +7109,36 @@ cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/rxn_op.c.o -MF CMakeFiles/rdkit.dir/rxn_op.c.o.d -o CMakeFiles/rdkit.dir/rxn_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/rxn_op.c [ 97%] Building C object Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKITVER=\"007600\" -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_INCHI_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_MOLINTERCHANGE_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_TOOLKIT_VERSION=\"2024.09.6\" -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdkit_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/usr/include/postgresql -I/usr/include/postgresql/17/server -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/include/freetype2 -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -fPIC -MD -MT Code/PgSQL/rdkit/CMakeFiles/rdkit.dir/sfp_op.c.o -MF CMakeFiles/rdkit.dir/sfp_op.c.o.d -o CMakeFiles/rdkit.dir/sfp_op.c.o -c /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/sfp_op.c -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/MolBundle.cpp -[ 97%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp -[ 97%] Linking CXX shared library librdkit.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/lib /usr/lib/aarch64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/sql -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/data -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/expected +/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp: In function 'void* makeAvalonBFP(CROMol, bool, unsigned int)': +/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:38: warning: unused parameter 'data' [-Wunused-parameter] + 1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, + | ~~~~~~~^~~~ +/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1627:49: warning: unused parameter 'isQuery' [-Wunused-parameter] + 1627 | extern "C" CBfp makeAvalonBFP(CROMol data, bool isQuery, + | ~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/adapter.cpp:1628:44: warning: unused parameter 'bitFlags' [-Wunused-parameter] + 1628 | unsigned int bitFlags) { + | ~~~~~~~~~~~~~^~~~~~~~ +[ 97%] Linking CXX executable moldraw2DTestCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 97%] Built target rdkit -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-202409.6/Code/GraphMol/Wrap/StereoGroup.cpp -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/SubstanceGroup.cpp -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/Chirality.cpp +[ 97%] Built target moldraw2DTestCatch +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdMolStandardize.dir/link.d -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 CMakeFiles/rdMolStandardize.dir/Pipeline.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 97%] Built target rdMolStandardize +[ 97%] Linking CXX executable generalizedSubstructCatch +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdGeneralizedSubstruct.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 97%] Built target rdGeneralizedSubstruct +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/generalizedSubstructCatch.dir/link.d CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 97%] Built target generalizedSubstructCatch [ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/SubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -7114,43 +7147,38 @@ [ 97%] Built target SubstructLibrary make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/depend make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.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-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-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-202409.6/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build.make Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/catch_tests.cpp +[ 98%] Building CXX object Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SynthonSpaceSearch/CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -MF CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o.d -o CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/catch_tests.cpp +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp -[ 99%] Linking CXX executable moldraw2DTestCatch -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/moldraw2DTestCatch.dir/link.d CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitCIPLabeler.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 99%] Built target moldraw2DTestCatch +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [ 99%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/RGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl @@ -7162,51 +7190,69 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202409.6 /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake "--color=" +[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/build -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp -[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o -MF CMakeFiles/gaExample.dir/GaExample.cpp.o.d -o CMakeFiles/gaExample.dir/GaExample.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/GaExample.cpp cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp [ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_NUMPY_DYN_LINK -DBOOST_NUMPY_NO_LIB -DBOOST_PYTHON_DYN_LINK -DBOOST_PYTHON_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -I/usr/lib/aarch64-linux-gnu/python3-numpy/numpy/_core/include -isystem /usr/include/python3.13 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp -[ 99%] Linking CXX executable substructLibraryCatchTest -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202409.6/External -I/build/reproducible-path/rdkit-202409.6/Code -I/build/reproducible-path/rdkit-202409.6/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/gaExample.dir/GaExample.cpp.o -MF CMakeFiles/gaExample.dir/GaExample.cpp.o.d -o CMakeFiles/gaExample.dir/GaExample.cpp.o -c /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/GaExample.cpp +[ 99%] Linking CXX shared library librdkit.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkit.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,--dependency-file=CMakeFiles/rdkit.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,librdkit.so -o librdkit.so CMakeFiles/rdkit.dir/adapter.cpp.o CMakeFiles/rdkit.dir/bfp_op.c.o CMakeFiles/rdkit.dir/cache.c.o CMakeFiles/rdkit.dir/guc.c.o CMakeFiles/rdkit.dir/low_gist.c.o CMakeFiles/rdkit.dir/mol_op.c.o CMakeFiles/rdkit.dir/rdkit_gist.c.o CMakeFiles/rdkit.dir/bfp_gist.c.o CMakeFiles/rdkit.dir/bfp_gin.c.o CMakeFiles/rdkit.dir/bitstring.c.o CMakeFiles/rdkit.dir/rdkit_io.c.o CMakeFiles/rdkit.dir/rxn_op.c.o CMakeFiles/rdkit.dir/sfp_op.c.o -L/build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/lib /usr/lib/aarch64-linux-gnu/libpq.so ../../../lib/libRDKitRDInchiLib.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libinchi.so ../../../lib/libRDKitMolInterchange.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolDraw2D.so.1.2024.09.6 ../../../lib/libRDKitMolHash.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitDescriptors.so.1.2024.09.6 ../../../lib/libRDKitPartialCharges.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/sql /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/sql +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/data /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/data +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit && /usr/bin/cmake -E copy_directory /build/reproducible-path/rdkit-202409.6/Code/PgSQL/rdkit/expected /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/PgSQL/rdkit/expected make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 99%] Built target substructLibraryCatchTest +[ 99%] Built target rdkit +[ 99%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 +[ 99%] Linking CXX executable gaExample +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 99%] Built target testRGroupDecompInternals +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 99%] Built target gaExample [ 99%] Linking CXX executable substructLibraryTest cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryTest.dir/link.d CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target substructLibraryTest +[ 99%] Linking CXX executable substructLibraryCatchTest +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/substructLibraryCatchTest.dir/link.d CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 99%] Built target substructLibraryCatchTest [ 99%] Linking CXX executable testSynthonSpaceSubstructureSearch cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SynthonSpaceSearch && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.txt --verbose=1 /usr/bin/ld: CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o: in function `CATCH2_INTERNAL_TEST_20()': @@ -7214,41 +7260,26 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testSynthonSpaceSubstructureSearch.dir/link.d CMakeFiles/testSynthonSpaceSubstructureSearch.dir/substructure_search_catch_tests.cpp.o -o testSynthonSpaceSubstructureSearch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../lib/libRDKitSynthonSpaceSearch.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target testSynthonSpaceSubstructureSearch -[ 99%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecompInternals.dir/link.d CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 99%] Built target testRGroupDecompInternals -[ 99%] Linking CXX executable gaExample -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaExample.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/gaExample.dir/link.d CMakeFiles/gaExample.dir/GaExample.cpp.o -o gaExample ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.83.0 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 99%] Built target gaExample -[ 99%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdchem.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2024.09.6 ../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[ 99%] Built target rdchem [ 99%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/rgroupCatchTests.dir/link.d CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target rgroupCatchTests +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdRGroupDecomposition.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../../lib/libRDKitga.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [ 99%] Built target rdRGroupDecomposition +[ 99%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' +[ 99%] Built target testRGroupDecomp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,--dependency-file=CMakeFiles/rdSubstructLibrary.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2024.09.6 ../../../../lib/libRDKitRDBoost.so.1.2024.09.6 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2024.09.6 ../../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../../lib/libRDKitFileParsers.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../../lib/libRDKitAlignment.so.1.2024.09.6 ../../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../../lib/libRDKitDataStructs.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_numpy313.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 ../../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' [100%] Built target rdSubstructLibrary -[100%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202409.6=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/testRGroupDecomp.dir/link.d CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2024.09.6 ../../../lib/libRDKitFMCS.so.1.2024.09.6 ../../../lib/libRDKitga.so.1.2024.09.6 ../../../lib/libRDKitMolEnumerator.so.1.2024.09.6 ../../../lib/libRDKitTautomerQuery.so.1.2024.09.6 ../../../lib/libRDKitMolStandardize.so.1.2024.09.6 ../../../lib/libRDKitChemReactions.so.1.2024.09.6 ../../../lib/libRDKitFingerprints.so.1.2024.09.6 ../../../lib/libRDKitFileParsers.so.1.2024.09.6 ../../../lib/libRDKitChemTransforms.so.1.2024.09.6 ../../../lib/libRDKitDepictor.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2024.09.6 ../../../lib/libRDKitMolTransforms.so.1.2024.09.6 ../../../lib/libRDKitEigenSolvers.so.1.2024.09.6 ../../../lib/libRDKitAlignment.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitFilterCatalog.so.1.2024.09.6 ../../../lib/libRDKitSubstructMatch.so.1.2024.09.6 ../../../lib/libRDKitGenericGroups.so.1.2024.09.6 ../../../lib/libRDKitSmilesParse.so.1.2024.09.6 ../../../lib/libRDKitSubgraphs.so.1.2024.09.6 ../../../lib/libRDKitGraphMol.so.1.2024.09.6 ../../../lib/libRDKitRDGeometryLib.so.1.2024.09.6 ../../../lib/libRDKitDataStructs.so.1.2024.09.6 ../../../lib/libRDKitCatalogs.so.1.2024.09.6 ../../../lib/libRDKitRDGeneral.so.1.2024.09.6 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so.1.83.0 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' -[100%] Built target testRGroupDecomp make[3]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' @@ -12878,7 +12909,7 @@ resolving references... /build/reproducible-path/rdkit-202409.6/Docs/Book/GettingStartedWithContributing.md:273: WARNING: 'myst' cross-reference target not found: 'building-rdkit-for-development' [myst.xref_missing] -WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] +WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NameResolutionError(": Failed to resolve 'img.shields.io' ([Errno -3] Temporary failure in name resolution)"))] processing RDKit.tex: done writing... done copying images... [ 1%] images/Cc1ccccc1.png @@ -15095,41 +15126,41 @@ 12: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testBV.py" 12: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 -3: [05:51:04] Testing Github940: property dictionaries leaking memory -3: [05:51:04] done +3: [15:23:02] Testing Github940: property dictionaries leaking memory +3: [15:23:02] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.00029 s -3: dynamic boost any:0.001026 s +3: static boost any:0.000271 s +3: dynamic boost any:0.001034 s 3: static RDAny:0.000124 s -3: dynamic RDAny:0.000994 s +3: dynamic RDAny:0.000974 s 3: static RDValue:0 s 3: dynamic RDValue:0.000155 s 3: deleted! -3: [05:51:04] ------------------------------------- -3: [05:51:04] Testing String Pickle Roundtrips. -3: [05:51:04] done -3: [05:51:04] ------------------------------------- -3: [05:51:04] Testing conversion of vect to string. -3: [05:51:04] done -3: [05:51:04] ------------------------------------- -3: [05:51:04] Testing returning const references. -3: [05:51:04] any cast -3: [05:51:04] done: 0.000803 300000 -3: [05:51:04] copy -3: [05:51:04] done: 0.000836 300000 -3: [05:51:04] ref -3: [05:51:04] done: 0.000802 300000 -3: [05:51:04] dict -3: [05:51:04] done: 0.002025 300000 -3: [05:51:04] ref with hasVal -3: [05:51:04] done: 0.001306 300000 -3: [05:51:04] done -3: [05:51:04] ------------------------------------- -3: [05:51:04] Testing dict update. -3: [05:51:04] done +3: [15:23:02] ------------------------------------- +3: [15:23:02] Testing String Pickle Roundtrips. +3: [15:23:02] done +3: [15:23:02] ------------------------------------- +3: [15:23:02] Testing conversion of vect to string. +3: [15:23:02] done +3: [15:23:02] ------------------------------------- +3: [15:23:02] Testing returning const references. +3: [15:23:02] any cast +3: [15:23:02] done: 0.000815 300000 +3: [15:23:02] copy +3: [15:23:02] done: 0.000853 300000 +3: [15:23:02] ref +3: [15:23:02] done: 0.000801 300000 +3: [15:23:02] dict +3: [15:23:02] done: 0.001956 300000 +3: [15:23:02] ref with hasVal +3: [15:23:02] done: 0.001306 300000 +3: [15:23:02] done +3: [15:23:02] ------------------------------------- +3: [15:23:02] Testing dict update. +3: [15:23:02] done 3: deleted! 3: deleted! 3: deleted! @@ -15148,34 +15179,30 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [05:51:04] +5: [15:23:02] 5: ----------------------------------------- -5: [05:51:04] Finished: testPushAndPop() -5: [05:51:04] +5: [15:23:02] Finished: testPushAndPop() +5: [15:23:02] 5: ----------------------------------------- -5: [05:51:04] +5: [15:23:02] 5: ----------------------------------------- -6: Randomness seeded to: 185385396 -6: =============================================================================== -6: All tests passed (32 assertions in 2 test cases) -6: -8: [05:51:04] pass -8: [05:51:04] v3 4 -8: [05:51:04] v4 5 -8: [05:51:04] SPARSE ----------------------------------- -8: [05:51:04] Set 10: 0 -8: [05:51:04] Set 11: 0 -8: [05:51:04] Set 14: 0 -8: [05:51:04] Set 10: 1 -8: [05:51:04] Get 14: 1 -8: [05:51:04] Num: 20 -8: [05:51:04] NumOn: 3 -8: [05:51:04] NumOff: 17 +8: [15:23:02] pass +8: [15:23:02] v3 4 +8: [15:23:02] v4 5 +8: [15:23:02] SPARSE ----------------------------------- +8: [15:23:02] Set 10: 0 +8: [15:23:02] Set 11: 0 +8: [15:23:02] Set 14: 0 +8: [15:23:02] Set 10: 1 +8: [15:23:02] Get 14: 1 +8: [15:23:02] Num: 20 +8: [15:23:02] NumOn: 3 +8: [15:23:02] NumOff: 17 8: 10, 11, 14, -8: [05:51:04] t2[19]: 0 -8: [05:51:04] t2[14]: 1 -8: [05:51:04] t2[19]: 0 -8: [05:51:04] t2[14]: 0 +8: [15:23:02] t2[19]: 0 +8: [15:23:02] t2[14]: 1 +8: [15:23:02] t2[19]: 0 +8: [15:23:02] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15183,20 +15210,22 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [05:51:04] Explicit ---------------------------------- -8: [05:51:04] Set 10: 0 -8: [05:51:04] Set 11: 0 -8: [05:51:04] Set 14: 0 -8: [05:51:04] Set 10: 1 -8: [05:51:04] Get 14: 1 -8: [05:51:04] Num: 20 -8: [05:51:04] NumOn: 3 -8: [05:51:04] NumOff: 17 + 1/235 Test #3: testDict ............................... Passed 0.26 sec + 2/235 Test #4: testRDValue ............................ Passed 0.28 sec +8: [15:23:02] Explicit ---------------------------------- +8: [15:23:02] Set 10: 0 +8: [15:23:02] Set 11: 0 +8: [15:23:02] Set 14: 0 +8: [15:23:02] Set 10: 1 +8: [15:23:02] Get 14: 1 +8: [15:23:02] Num: 20 +8: [15:23:02] NumOn: 3 +8: [15:23:02] NumOff: 17 8: 10, 11, 14, -8: [05:51:04] t2[19]: 0 -8: [05:51:04] t2[14]: 1 -8: [05:51:04] t2[19]: 0 -8: [05:51:04] t2[14]: 0 +8: [15:23:02] t2[19]: 0 +8: [15:23:02] t2[14]: 1 +8: [15:23:02] t2[19]: 0 +8: [15:23:02] t2[14]: 0 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, 8: t1|t2: 10, 11, 14, 15, 17, @@ -15204,24 +15233,8 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except -8: [05:51:04] Done -8: [05:51:04] Test DiscreteValue Vectors 1 ---------------------------- -8: [05:51:04] Expected failure: Value out of range -8: [05:51:04] Expected failure: Value out of range -8: [05:51:04] Expected failure: Value out of range -8: [05:51:04] Expected failure: Value out of range -8: [05:51:04] Expected failure: Value out of range -8: [05:51:04] Test DiscreteValue Vectors 2 ------------------------------ -8: [05:51:04] Test DiscreteValue Vectors 3 --------------------------- -8: [05:51:04] Test DiscreteValue Operations ----------------------------- -8: [05:51:04] Test DiscreteValue Operations 2 -------------------------- -8: [05:51:04] Test SparseIntVect ------------------------------------ - 1/235 Test #3: testDict ............................... Passed 0.15 sec - 2/235 Test #4: testRDValue ............................ Passed 0.15 sec - 3/235 Test #6: dictTestsCatch ......................... Passed 0.12 sec - 4/235 Test #9: testFPB ................................ Passed 0.08 sec -8: [05:51:04] Test SparseIntVect Serialization -------------------------- -8: [05:51:04] Test BitVect Serialization ------------------------------- +8: [15:23:02] Done +8: [15:23:02] Test DiscreteValue Vectors 1 ---------------------------- test 13 Start 13: pyDiscreteValueVect @@ -15234,70 +15247,77 @@ 14: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testRealValueVect.py" 14: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 +8: [15:23:02] Expected failure: Value out of range +8: [15:23:02] Expected failure: Value out of range +8: [15:23:02] Expected failure: Value out of range +8: [15:23:02] Expected failure: Value out of range +8: [15:23:02] Expected failure: Value out of range +8: [15:23:02] Test DiscreteValue Vectors 2 ------------------------------ +8: [15:23:02] Test DiscreteValue Vectors 3 --------------------------- +8: [15:23:02] Test DiscreteValue Operations ----------------------------- +8: [15:23:02] Test DiscreteValue Operations 2 -------------------------- +8: [15:23:02] Test SparseIntVect ------------------------------------ +8: [15:23:02] Test SparseIntVect Serialization -------------------------- +8: [15:23:02] Test BitVect Serialization ------------------------------- +8: [15:23:02] Test BitVect to FPS ------------------------------- +8: [15:23:02] Test BitVect to binary string ------------------------------- +8: [15:23:02] Test Similarity Measures BitVect ------------------------------- +8: [15:23:02] Test Similarity Measures SparseBitVect ------------------------------- +8: [15:23:02] Test BitVect with all ones ------------------------------- +8: [15:23:02] Test Explicit BitVects: Concatenation Operation ------------------------------- +8: [15:23:02] Test bitmap operations ------------------------------- +8: [15:23:02] Test bitmaps as properties ------------------------------- +8: [15:23:02] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- + 3/235 Test #9: testFPB ................................ Passed 0.23 sec test 15 Start 15: pySparseIntVect 15: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testSparseIntVect.py" 15: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 15: Test timeout computed to be: 1500 +8: [15:23:02] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- +8: [15:23:02] Test RealValue Vectors 2: L1Norm ------------------------------- +8: [15:23:02] Test RealValue Vectors 3: Pickles ------------------------------- +8: [15:23:02] Test RealValue Vectors 4: Vector Operations ------------------------------- + 4/235 Test #8: testDataStructs ........................ Passed 0.27 sec test 16 Start 16: pyFPB 16: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DataStructs/Wrap/testFPB.py" 16: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 16: Test timeout computed to be: 1500 -8: [05:51:04] Test BitVect to FPS ------------------------------- -8: [05:51:04] Test BitVect to binary string ------------------------------- -8: [05:51:04] Test Similarity Measures BitVect ------------------------------- -8: [05:51:04] Test Similarity Measures SparseBitVect ------------------------------- -8: [05:51:04] Test BitVect with all ones ------------------------------- -8: [05:51:04] Test Explicit BitVects: Concatenation Operation ------------------------------- -8: [05:51:04] Test bitmap operations ------------------------------- -8: [05:51:04] Test bitmaps as properties ------------------------------- -8: [05:51:04] Test #3944: SparseIntVect copy constructor and assignment operators not clearing existing data------------------------------- -8: [05:51:04] Test RealValue Vectors 1: Constructors and Accessing Values ------------------------------- -8: [05:51:04] Test RealValue Vectors 2: L1Norm ------------------------------- -8: [05:51:04] Test RealValue Vectors 3: Pickles ------------------------------- -8: [05:51:04] Test RealValue Vectors 4: Vector Operations ------------------------------- -7: [05:51:04] should not be silent -7: [05:51:04] should not be silent -7: Randomness seeded to: 29658979 -7: [05:51:04] should not be silent -7: [05:51:04] should not be silent -7: [05:51:04] should not be silent -7: [05:51:04] should not be silent -7: [05:51:04] should not be silent -7: [05:51:04] should not be silent -7: [05:51:04] should not be silent -7: [05:51:04] should not be silent +7: [15:23:02] should not be silent +7: [15:23:02] should not be silent +7: Randomness seeded to: 3461035271 +7: [15:23:02] should not be silent +7: [15:23:02] should not be silent +7: [15:23:02] should not be silent +7: [15:23:02] should not be silent +7: [15:23:02] should not be silent +7: [15:23:02] should not be silent +7: [15:23:02] should not be silent +7: [15:23:02] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: - 5/235 Test #7: logTestsCatch .......................... Passed 0.19 sec - 6/235 Test #8: testDataStructs ........................ Passed 0.17 sec + 5/235 Test #7: logTestsCatch .......................... Passed 0.37 sec test 17 Start 17: testTransforms 17: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/testTransforms 17: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry 17: Test timeout computed to be: 1500 + 6/235 Test #10: testMultiFPB ........................... Passed 0.27 sec test 18 Start 18: testGrid 18: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/testGrid 18: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry 18: Test timeout computed to be: 1500 -11: Randomness seeded to: 1656817704 -11: =============================================================================== -11: All tests passed (3 assertions in 1 test case) -11: - 7/235 Test #11: catchDataStructs ....................... Passed 0.20 sec -test 19 - Start 19: testRealValueGrid - -19: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/testRealValueGrid -19: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry -19: Test timeout computed to be: 1500 +6: Randomness seeded to: 2382420890 +6: =============================================================================== +6: All tests passed (32 assertions in 2 test cases) +6: 17: **************************************** 17: testPointND 17: **************************************** @@ -15306,8 +15326,8 @@ 17: testPointOps2D 17: **************************************** 17: test12D -17: ref1: 0.370705 1.14845 ref2: 1.01493 4.48046 -17: pt1: 4.96096 2.86882 pt2: 0.0518594 3.36955 +17: ref1: 1.48105 2.06261 ref2: 2.68915 0.680788 +17: pt1: 2.8714 2.01527 pt2: 0.283449 1.1894 17: **************************************** 17: test23D 17: **************************************** @@ -15322,13 +15342,13 @@ 17: **************************************** 17: testFromQuaternion 17: **************************************** - 8/235 Test #17: testTransforms ......................... Passed 0.09 sec -test 20 - Start 20: geometryTestsCatch + 7/235 Test #17: testTransforms ......................... Passed 0.09 sec +test 19 + Start 19: testRealValueGrid -20: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch -20: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry -20: Test timeout computed to be: 1500 +19: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/testRealValueGrid +19: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry +19: Test timeout computed to be: 1500 18: *********************************************************** 18: Testing Grid 18: --------------------------------- @@ -15346,20 +15366,20 @@ 18: --------------------------------- 18: testUniformGridIndexing 18: - 9/235 Test #18: testGrid ............................... Passed 0.08 sec + 8/235 Test #6: dictTestsCatch ......................... Passed 0.49 sec +test 20 + Start 20: geometryTestsCatch + +20: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch +20: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry +20: Test timeout computed to be: 1500 + 9/235 Test #18: testGrid ............................... Passed 0.10 sec test 21 Start 21: testPyGeometry 21: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Geometry/Wrap/testGeometry.py" 21: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Geometry/Wrap 21: Test timeout computed to be: 1500 - 10/235 Test #10: testMultiFPB ........................... Passed 0.27 sec -test 22 - Start 22: testMatrices - -22: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/testMatrices -22: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics -22: Test timeout computed to be: 1500 19: *********************************************************** 19: Testing RealValueGrid3D 19: --------------------------------- @@ -15374,23 +15394,34 @@ 19: --------------------------------- 19: test4UniformRealValueGrid3DOps 19: - 11/235 Test #19: testRealValueGrid ...................... Passed 0.09 sec + 10/235 Test #19: testRealValueGrid ...................... Passed 0.11 sec +test 22 + Start 22: testMatrices + +22: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/testMatrices +22: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics +22: Test timeout computed to be: 1500 +11: Randomness seeded to: 3456364653 +11: =============================================================================== +11: All tests passed (3 assertions in 1 test case) +11: + 11/235 Test #11: catchDataStructs ....................... Passed 0.44 sec test 23 Start 23: testConrec 23: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/testConrec 23: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics 23: Test timeout computed to be: 1500 -22: [05:51:04] ----------------------------------------- -22: [05:51:04] Testing RDNumerics: vectors and matrices Code -22: [05:51:04] --------------------------------------- -22: [05:51:04] test1Vector -22: [05:51:04] --------------------------------------- -22: [05:51:04] test2Matrix -22: [05:51:04] --------------------------------------- -22: [05:51:04] test3SquareMatrix -22: [05:51:04] --------------------------------------- -22: [05:51:04] test4SymmMatrix +22: [15:23:03] ----------------------------------------- +22: [15:23:03] Testing RDNumerics: vectors and matrices Code +22: [15:23:03] --------------------------------------- +22: [15:23:03] test1Vector +22: [15:23:03] --------------------------------------- +22: [15:23:03] test2Matrix +22: [15:23:03] --------------------------------------- +22: [15:23:03] test3SquareMatrix +22: [15:23:03] --------------------------------------- +22: [15:23:03] test4SymmMatrix 12/235 Test #22: testMatrices ........................... Passed 0.07 sec test 24 Start 24: testAlignment @@ -15409,13 +15440,94 @@ 24: --------------------------------------- 24: testReflection 24: --------------------------------------- - 13/235 Test #24: testAlignment .......................... Passed 0.03 sec + 13/235 Test #24: testAlignment .......................... Passed 0.08 sec test 25 Start 25: pyAlignment 25: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/Numerics/Alignment/Wrap/testAlignment.py" 25: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap 25: Test timeout computed to be: 1500 +20: Randomness seeded to: 1929393727 +20: =============================================================================== +20: All tests passed (50 assertions in 5 test cases) +20: + 14/235 Test #20: geometryTestsCatch ..................... Passed 0.40 sec +test 26 + Start 26: testOptimizer + +26: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +26: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer +26: Test timeout computed to be: 1500 +26: ------------------------------------- +26: Testing linear search. +26: done +26: ------------------------------------- +26: Testing BFGS optimization. +26: done + 15/235 Test #26: testOptimizer .......................... Passed 0.04 sec +test 27 + Start 27: ForceFieldsCatch + +27: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch +27: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField +27: Test timeout computed to be: 1500 +23: Randomness seeded to: 1892244272 +23: =============================================================================== +23: All tests passed (76 assertions in 3 test cases) +23: + 16/235 Test #23: testConrec ............................. Passed 0.45 sec +test 28 + Start 28: testUFFForceField + +28: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField +28: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF +28: Test timeout computed to be: 1500 +28: ------------------------------------- +28: Unit tests for force field basics. +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF bond-stretch terms. +28: done +28: ------------------------------------- +28: Unit tests for basics of UFF angle terms. +28: done +28: ------------------------------------- +28: Unit tests for UFF angle-bend terms. +28: theta = 3.14159; theta0 = 3.14159 +28: theta = 2.094395, param1.theta0 = 2.094395 +28: done +28: ------------------------------------- +28: Test Simple UFF molecule optimizations. +28: done +28: ------------------------------------- +28: Unit tests for UFF nonbonded terms. +28: done +28: ------------------------------------- +28: Test UFF torsional terms. +28: done +28: ------------------------------------- +28: Test UFF Parameter objects +28: ------------------------------------- +28: Test Simple UFF molecule optimization, part 2. +28: done +28: ------------------------------------- +28: Test UFF Torsion Conflicts. +28: C 0.4783 -0.7477 -0.0753 +28: C -0.5465 -0.0176 0.3519 +28: C -0.5114 1.4472 0.0870 +28: H -1.5201 -0.4838 0.2485 +28: H 0.4696 1.8363 0.3367 +28: O -1.2618 1.9423 0.6934 +28: F -0.7163 1.6298 -0.9622 +28: done +28: ------------------------------------- +28: Unit tests for UFF distance constraint terms. +28: done +28: ------------------------------------- +28: Unit tests for all UFF constraint terms. 1: core 1: RDKit 2D 1: @@ -15450,6 +15562,10 @@ 1: 7 1 1 0 1: M END 1: +27: Randomness seeded to: 536328395 +27: =============================================================================== +27: All tests passed (20 assertions in 2 test cases) +27: 1: templated 1: RDKit 2D 1: @@ -15828,6 +15944,13 @@ 1: 5 7 1 0 1: M END 1: + 17/235 Test #27: ForceFieldsCatch ....................... Passed 0.56 sec +test 29 + Start 29: testMMFFForceField + +29: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +29: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF +29: Test timeout computed to be: 1500 1: test1 1: RDKit 2D 1: @@ -15873,111 +15996,402 @@ 1: 2 5 1 0 1: M END 1: -20: Randomness seeded to: 2944361015 -20: =============================================================================== -20: All tests passed (50 assertions in 5 test cases) -20: - 14/235 Test #20: geometryTestsCatch ..................... Passed 0.24 sec -test 26 - Start 26: testOptimizer - -26: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -26: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/Numerics/Optimizer -26: Test timeout computed to be: 1500 -26: ------------------------------------- -26: Testing linear search. -26: done -26: ------------------------------------- -26: Testing BFGS optimization. -26: done - 15/235 Test #26: testOptimizer .......................... Passed 0.02 sec -test 27 - Start 27: ForceFieldsCatch - -27: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/ForceFieldsCatch -27: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField -27: Test timeout computed to be: 1500 -23: Randomness seeded to: 2267067539 -23: =============================================================================== -23: All tests passed (76 assertions in 3 test cases) -23: -27: Randomness seeded to: 3176956677 -27: =============================================================================== -27: All tests passed (20 assertions in 2 test cases) -27: - 16/235 Test #23: testConrec ............................. Passed 0.25 sec -test 28 - Start 28: testUFFForceField - -28: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField -28: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/UFF -28: Test timeout computed to be: 1500 - 17/235 Test #27: ForceFieldsCatch ....................... Passed 0.09 sec -test 29 - Start 29: testMMFFForceField - -29: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -29: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/MMFF -29: Test timeout computed to be: 1500 -28: ------------------------------------- -28: Unit tests for force field basics. 28: done 28: ------------------------------------- -28: Unit tests for basics of UFF bond-stretch terms. -28: done -28: ------------------------------------- -28: Unit tests for UFF bond-stretch terms. -28: done -28: ------------------------------------- -28: Unit tests for basics of UFF angle terms. -28: done -28: ------------------------------------- -28: Unit tests for UFF angle-bend terms. -28: theta = 3.14159; theta0 = 3.14159 -28: theta = 2.094395, param1.theta0 = 2.094395 -28: done -28: ------------------------------------- -28: Test Simple UFF molecule optimizations. -28: done -28: ------------------------------------- -28: Unit tests for UFF nonbonded terms. -28: done -28: ------------------------------------- -28: Test UFF torsional terms. -28: done -28: ------------------------------------- -28: Test UFF Parameter objects -28: ------------------------------------- -28: Test Simple UFF molecule optimization, part 2. -28: done -28: ------------------------------------- -28: Test UFF Torsion Conflicts. -28: C 0.4783 -0.7477 -0.0753 -28: C -0.5465 -0.0176 0.3519 -28: C -0.5114 1.4472 0.0870 -28: H -1.5201 -0.4838 0.2485 -28: H 0.4696 1.8363 0.3367 -28: O -1.2618 1.9423 0.6934 -28: F -0.7163 1.6298 -0.9622 -28: done -28: ------------------------------------- -28: Unit tests for UFF distance constraint terms. -28: done -28: ------------------------------------- -28: Unit tests for all UFF constraint terms. +28: Unit tests for copying UFF ForceFields. 29: ------------------------------------- 29: Official MMFF validation suite. +28: done +28: ------------------------------------- +28: Unit test for UFF butane scan. +16: ......... +16: ---------------------------------------------------------------------- +16: Ran 9 tests in 0.126s +16: +16: OK +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.119s +13: +13: OK 14: ...... 14: ---------------------------------------------------------------------- -14: Ran 6 tests in 0.015s +14: Ran 6 tests in 0.023s 14: 14: OK +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.080s +15: +15: OK +25: ..... +25: ---------------------------------------------------------------------- +25: Ran 5 tests in 0.053s +25: +25: OK +25: Testing Alignment Wrapper code: + 18/235 Test #13: pyDiscreteValueVect .................... Passed 1.51 sec +test 30 + Start 30: pyForceFieldConstraints + +30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap/testConstraints.py" +30: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap +30: Test timeout computed to be: 1500 + 19/235 Test #16: pyFPB .................................. Passed 1.46 sec +test 31 + Start 31: testDistGeom + +31: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom +31: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom +31: Test timeout computed to be: 1500 + 20/235 Test #14: pyRealValueVect ........................ Passed 1.58 sec +test 32 + Start 32: pyDistGeom + +32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/rough_test.py" +32: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap +32: Test timeout computed to be: 1500 + 21/235 Test #25: pyAlignment ............................ Passed 1.12 sec +test 33 + Start 33: graphmolTest1 + +33: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +33: Test timeout computed to be: 1500 +31: *********************************************************** +31: test1 +31: *********************************************************** +31: testIssue216 +31: Rows: 4 Columns: 4 +31: 0 1 1 1 +31: 1 0 1 1 +31: 1 1 0 1 +31: 1 1 1 0 +31: *********************************************************** +31: + 22/235 Test #31: testDistGeom ........................... Passed 0.08 sec +test 34 + Start 34: graphmolcpTest + +34: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest +34: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +34: Test timeout computed to be: 1500 +21: .................... +21: ---------------------------------------------------------------------- +21: Ran 20 tests in 0.195s +21: +21: OK +21: Testing Geometry wrapper + 23/235 Test #15: pySparseIntVect ........................ Passed 1.58 sec +test 35 + Start 35: graphmolqueryTest + +35: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest +35: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 28: done -28: ------------------------------------- -28: Unit tests for copying UFF ForceFields. -28: done -28: ------------------------------------- -28: Unit test for UFF butane scan. +33: Atoms: +33: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: +33: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: +33: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: +33: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: +33: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: +33: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: +33: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: +33: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: arom?: 1 query: AtomAtomicNum +33: 8 22 Ti chg: 0 deg: 1 exp: N/A imp: N/A hyb: +33: Bonds: +33: 0 0->1 order: 1 +33: 1 1->2 order: 2 +33: 2 2->3 order: 1 +33: 3 0->4 order: 1 +33: 4 5->6 order: 3 +33: 5 6->7 order: 1 +33: 6 7->8 order: 2 +33: [15:23:04] +33: +33: **** + 24/235 Test #28: testUFFForceField ...................... Passed 0.86 sec +test 36 + Start 36: graphmolMolOpsTest + +36: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +36: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +33: Pre-condition Violation +33: bond already exists +33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp +33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x0000AAAADD78B7A0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] +33: +33: **** +33: Pre-condition Violation +33: bond already exists +33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp +33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x0000AAAADD78B9C0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] +33: +33: **** +33: Pre-condition Violation +33: attempt to add self-bond +33: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp +33: Failed Expression: atomIdx1 != atomIdx2 +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x0000AAAADD78BAB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] +33: +33: **** +33: Pre-condition Violation +33: bond already exists +33: Violation occurred on line 419 in file ./Code/GraphMol/ROMol.cpp +33: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x0000AAAADD78BAF4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] +33: +33: **** +33: Pre-condition Violation +33: attempt to add self-bond +33: Violation occurred on line 417 in file ./Code/GraphMol/ROMol.cpp +33: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +33: 3# 0x0000AAAADD78BC3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAADD783DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 7# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] Explicit valence for atom # 0 B, 4, is greater than permitted +33: [15:23:04] Explicit valence for atom # 0 B, 4, is greater than permitted +33: [15:23:04] +33: +33: **** +33: Post-condition Violation +33: Element 'Xx' not found +33: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +33: Failed Expression: anum > -1 +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAADD7B6868 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000AAAADD79A358 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 5# 0x0000AAAADD783DE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 6# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 8# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] ------------------------------------- +33: [15:23:04] Test github381: thread-safe initialization of the periodic table +35: [15:23:04] ---------------------- Test1 + 25/235 Test #21: testPyGeometry ......................... Passed 1.47 sec +test 37 + Start 37: graphmoltestChirality + +37: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality +37: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +34: +34: +34: +34: COPY +33: [15:23:04] done +33: [15:23:04] ------------------------------------- +33: [15:23:04] Test github1041: Segfault for atom with no owner (expect some warnings) +33: [15:23:04] +33: +33: **** +33: Pre-condition Violation +33: no owner +33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +33: Failed Expression: dp_mol +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# 0x0000AAAADD7AAA58 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAADD783E0C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] +33: +33: **** +33: Pre-condition Violation +33: no owner +33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h +33: Failed Expression: dp_mol +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# 0x0000AAAADD7AAE34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAADD783E0C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] done +33: [15:23:04] ------------------------------------- +33: [15:23:04] Test github1041: Segfault for atom with no owner (expect some warnings) +33: [15:23:04] +33: +33: **** +33: Pre-condition Violation +33: no owner +33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h +33: Failed Expression: dp_mol +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# 0x0000AAAADD7AAA58 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAADD783E10 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] +33: +33: **** +33: Pre-condition Violation +33: no owner +33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h +33: Failed Expression: dp_mol +33: ---------- +33: Stacktrace: +33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +33: 2# 0x0000AAAADD7AAE34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 3# 0x0000AAAADD783E10 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: 4# 0x0000FFFFA793229C in /lib/aarch64-linux-gnu/libc.so.6 +33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +33: 6# 0x0000AAAADD783EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 +33: ---------- +33: **** +33: +33: [15:23:04] done +33: [15:23:04] ------------------------------------- +33: [15:23:04] Test github1453: RWMol.clear() should reset the numBonds count. +33: [15:23:04] done +33: [15:23:04] ------------------------------------- +33: [15:23:04] Test range-based for loops. +33: [15:23:04] done +33: [15:23:04] ------------------------------------- +33: [15:23:04] Test github1642: Atom index type is too low for big molecules. +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test2 +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test3 + 26/235 Test #34: graphmolcpTest ......................... Passed 0.16 sec +test 38 + Start 38: graphmoltestPickler + +38: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler +38: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test4 +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test5 +35: [15:23:04] Done! +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test issue 2892580 +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test github issue 53: query molecules not matching [R] +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test queries using qualifiers instead of == +35: [15:23:04] Done! +36: 1 1 2 +36: 1 1 1 +36: 2 1 0.75 +35: [15:23:04] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +35: [15:23:04] Done! +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing String Pickle Roundtrips. +35: [15:23:04] ---------------------- Test extra atom queries +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test extra bond queries +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test num heteroatom neighbor queries +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test atom type queries +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +35: [15:23:04] Done! +35: [15:23:04] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +35: [15:23:04] Done! + 27/235 Test #35: graphmolqueryTest ...................... Passed 0.15 sec +test 39 + Start 39: graphmoltestPicklerGlobalSetting + +39: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +39: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 1: cyclosporine a 1: RDKit 2D 1: @@ -16154,11 +16568,6 @@ 1: 46 3 1 0 1: M END 1: -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.106s -15: -15: OK 1: single-double 1: RDKit 2D 1: @@ -16223,18 +16632,6 @@ 1: 9 10 1 0 1: M END 1: -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.043s -13: -13: OK - 18/235 Test #14: pyRealValueVect ........................ Passed 0.65 sec -test 30 - Start 30: pyForceFieldConstraints - -30: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ForceField/Wrap/testConstraints.py" -30: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ForceField/Wrap -30: Test timeout computed to be: 1500 1: admntn 1: RDKit 2D 1: @@ -16263,6 +16660,8 @@ 1: 10 2 1 0 1: M END 1: +39: [15:23:04] done +36: path: 2 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: @@ -16272,547 +16671,128 @@ 1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan O 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan O 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 -1: 1 2 1 0 -1: 2 3 1 0 -1: 2 4 2 0 -1: 4 5 1 0 -1: 5 6 3 0 -1: 6 7 1 0 -1: 7 8 2 0 -1: 8 9 1 0 -1: 9 10 3 0 -1: 10 11 1 0 -1: 11 12 2 0 -1: 12 13 1 0 -1: 13 14 3 0 -1: 14 15 1 0 -1: 15 16 2 0 -1: 16 17 1 0 -1: 16 18 1 0 -1: 12 19 1 0 -1: 19 20 2 0 -1: 20 21 1 0 -1: 20 22 1 0 -1: 19 23 1 0 -1: 23 24 3 0 -1: 24 25 1 0 -1: 25 26 1 0 -1: 26 27 2 0 -1: 27 28 2 0 -1: 26 29 1 0 -1: 29 30 3 0 -1: 8 31 1 0 -1: 31 32 2 0 -1: 32 33 1 0 -1: 32 34 1 0 -1: 31 35 1 0 -1: 35 36 3 0 -1: 36 37 1 0 -1: 37 38 2 0 -1: 37 39 1 0 -1: 39 40 2 0 -1: 40 41 1 0 -1: 40 42 1 0 -1: 39 4 1 0 -1: 15 7 1 0 -1: 30 11 1 0 -1: M END -1: -16: ......... -16: ---------------------------------------------------------------------- -16: Ran 9 tests in 0.098s -16: -16: OK - 19/235 Test #15: pySparseIntVect ........................ Passed 0.68 sec -test 31 - Start 31: testDistGeom - -31: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom -31: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom -31: Test timeout computed to be: 1500 - 20/235 Test #1: testCoordGen ........................... Passed 0.93 sec - 21/235 Test #13: pyDiscreteValueVect .................... Passed 0.75 sec -test 32 - Start 32: pyDistGeom - -32: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/DistGeom/Wrap/rough_test.py" -32: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/DistGeom/Wrap -32: Test timeout computed to be: 1500 -test 33 - Start 33: graphmolTest1 - -33: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -33: Test timeout computed to be: 1500 -31: *********************************************************** -31: test1 -31: *********************************************************** -31: testIssue216 -31: Rows: 4 Columns: 4 -31: 0 1 1 1 -31: 1 0 1 1 -31: 1 1 0 1 -31: 1 1 1 0 -31: *********************************************************** -31: -25: ..... -25: ---------------------------------------------------------------------- -25: Ran 5 tests in 0.022s -25: -25: OK -25: Testing Alignment Wrapper code: - 22/235 Test #31: testDistGeom ........................... Passed 0.05 sec -test 34 - Start 34: graphmolcpTest - -34: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest -34: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -34: Test timeout computed to be: 1500 - 23/235 Test #16: pyFPB .................................. Passed 0.75 sec -test 35 - Start 35: graphmolqueryTest - -35: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest -35: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -34: -34: -34: -34: COPY -33: Atoms: -33: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: -33: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: -33: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: -33: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: -33: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: -33: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: -33: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: -33: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: arom?: 1 query: AtomAtomicNum -33: 8 22 Ti chg: 0 deg: 1 exp: N/A imp: N/A hyb: -33: Bonds: -33: 0 0->1 order: 1 -33: 1 1->2 order: 2 -33: 2 2->3 order: 1 -33: 3 0->4 order: 1 -33: 4 5->6 order: 3 -33: 5 6->7 order: 1 -33: 6 7->8 order: 2 - 24/235 Test #34: graphmolcpTest ......................... Passed 0.06 sec -test 36 - Start 36: graphmolMolOpsTest - -36: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -36: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -28: done -35: [05:51:05] ---------------------- Test1 -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test2 -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test3 -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test4 -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test5 -35: [05:51:05] Done! -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test issue 2892580 -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test github issue 53: query molecules not matching [R] -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test queries using qualifiers instead of == -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test extra atom queries -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test extra bond queries -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test num heteroatom neighbor queries -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test atom type queries -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -35: [05:51:05] Done! -35: [05:51:05] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -35: [05:51:05] Done! -21: .................... -21: ---------------------------------------------------------------------- -21: Ran 20 tests in 0.092s -21: -21: OK -21: Testing Geometry wrapper -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: bond already exists -33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp -33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAAC488B7A0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAAC4883DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: - 25/235 Test #28: testUFFForceField ...................... Passed 0.38 sec - 26/235 Test #35: graphmolqueryTest ...................... Passed 0.05 sec -test 37 - Start 37: graphmoltestChirality - -37: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality -37: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 -test 38 - Start 38: graphmoltestPickler - -38: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler -38: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: bond already exists -33: Violation occurred on line 499 in file ./Code/GraphMol/RWMol.cpp -33: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAAC488B9C0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAAC4883DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: attempt to add self-bond -33: Violation occurred on line 498 in file ./Code/GraphMol/RWMol.cpp -33: Failed Expression: atomIdx1 != atomIdx2 -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAAC488BAB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAAC4883DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: bond already exists -33: Violation occurred on line 419 in file ./Code/GraphMol/ROMol.cpp -33: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAAC488BAF4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAAC4883DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: attempt to add self-bond -33: Violation occurred on line 417 in file ./Code/GraphMol/ROMol.cpp -33: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -33: 3# 0x0000AAAAC488BC3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAAC4883DDC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] Explicit valence for atom # 0 B, 4, is greater than permitted -33: [05:51:05] Explicit valence for atom # 0 B, 4, is greater than permitted -33: [05:51:05] -33: -33: **** -33: Post-condition Violation -33: Element 'Xx' not found -33: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -33: Failed Expression: anum > -1 -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAAC48B6868 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000AAAAC489A358 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 5# 0x0000AAAAC4883DE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 6# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 8# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] ------------------------------------- -33: [05:51:05] Test github381: thread-safe initialization of the periodic table -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.040s -2: -2: OK - 27/235 Test #25: pyAlignment ............................ Passed 0.59 sec -test 39 - Start 39: graphmoltestPicklerGlobalSetting - -39: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -39: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 -36: 1 1 2 -36: 1 1 1 -36: 2 1 0.75 -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing String Pickle Roundtrips. -33: [05:51:05] done -33: [05:51:05] ------------------------------------- -33: [05:51:05] Test github1041: Segfault for atom with no owner (expect some warnings) -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: no owner -33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -33: Failed Expression: dp_mol -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x0000AAAAC48AAA58 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAAC4883E0C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: no owner -33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h -33: Failed Expression: dp_mol -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x0000AAAAC48AAE34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAAC4883E0C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] done -33: [05:51:05] ------------------------------------- -33: [05:51:05] Test github1041: Segfault for atom with no owner (expect some warnings) -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: no owner -33: Violation occurred on line 146 in file ./Code/GraphMol/Atom.h -33: Failed Expression: dp_mol -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x0000AAAAC48AAA58 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAAC4883E10 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] -33: -33: **** -33: Pre-condition Violation -33: no owner -33: Violation occurred on line 187 in file ./Code/GraphMol/Bond.h -33: Failed Expression: dp_mol -33: ---------- -33: Stacktrace: -33: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -33: 2# 0x0000AAAAC48AAE34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 3# 0x0000AAAAC4883E10 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: 4# 0x0000FFFF89C8229C in /lib/aarch64-linux-gnu/libc.so.6 -33: 5# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -33: 6# 0x0000AAAAC4883EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 -33: ---------- -33: **** -33: -33: [05:51:05] done -33: [05:51:05] ------------------------------------- -33: [05:51:05] Test github1453: RWMol.clear() should reset the numBonds count. -33: [05:51:05] done -33: [05:51:05] ------------------------------------- -33: [05:51:05] Test range-based for loops. -33: [05:51:05] done -33: [05:51:05] ------------------------------------- -33: [05:51:05] Test github1642: Atom index type is too low for big molecules. - 28/235 Test #21: testPyGeometry ......................... Passed 0.75 sec +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan O 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan O 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan C 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: nan nan nan H 0 0 0 0 0 0 0 0 0 0 0 0 +1: 1 2 1 0 +1: 2 3 1 0 +1: 2 4 2 0 +1: 4 5 1 0 +1: 5 6 3 0 +1: 6 7 1 0 +1: 7 8 2 0 +1: 8 9 1 0 +1: 9 10 3 0 +1: 10 11 1 0 +1: 11 12 2 0 +1: 12 13 1 0 +1: 13 14 3 0 +1: 14 15 1 0 +1: 15 16 2 0 +1: 16 17 1 0 +1: 16 18 1 0 +1: 12 19 1 0 +1: 19 20 2 0 +1: 20 21 1 0 +1: 20 22 1 0 +1: 19 23 1 0 +1: 23 24 3 0 +1: 24 25 1 0 +1: 25 26 1 0 +1: 26 27 2 0 +1: 27 28 2 0 +1: 26 29 1 0 +1: 29 30 3 0 +1: 8 31 1 0 +1: 31 32 2 0 +1: 32 33 1 0 +1: 32 34 1 0 +1: 31 35 1 0 +1: 35 36 3 0 +1: 36 37 1 0 +1: 37 38 2 0 +1: 37 39 1 0 +1: 39 40 2 0 +1: 40 41 1 0 +1: 40 42 1 0 +1: 39 4 1 0 +1: 15 7 1 0 +1: 30 11 1 0 +1: M END +1: +37: -------------------------- +37: -------------------------- +37: C/C=C/C(C)Cl +36: [15:23:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +36: [15:23:04] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +36: [15:23:04] Explicit valence for atom # 0 B, 5, is greater than permitted +36: [15:23:04] Explicit valence for atom # 1 C, 5, is greater than permitted + 28/235 Test #39: graphmoltestPicklerGlobalSetting ....... Passed 0.08 sec test 40 Start 40: graphmolIterTest 40: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest 40: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 -36: path: 2 -36: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -36: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -37: -------------------------- -37: -------------------------- -37: C/C=C/C(C)Cl -39: [05:51:05] done - 29/235 Test #39: graphmoltestPicklerGlobalSetting ....... Passed 0.08 sec -test 41 - Start 41: hanoiTest - -41: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest -41: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -36: [05:51:05] Explicit valence for atom # 0 B, 5, is greater than permitted -36: [05:51:05] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [05:51:05] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [05:51:05] Explicit valence for atom # 1 C, 5, is greater than permitted -36: [05:51:05] Explicit valence for atom # 1 Si, 7, is greater than permitted - 30/235 Test #2: pyCoordGen ............................. Passed 1.16 sec - 31/235 Test #40: graphmolIterTest ....................... Passed 0.05 sec -test 42 - Start 42: graphmolMemTest1 - -42: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 -42: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 -test 43 - Start 43: resMolSupplierTest - -43: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest -43: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 -41: [05:51:05] Testing the hanoi sort -41: [05:51:05] populating vectors - 32/235 Test #42: graphmolMemTest1 ....................... Passed 0.02 sec -test 44 - Start 44: molBundleTest - -44: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest -44: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 -32: ...... -32: ---------------------------------------------------------------------- -32: Ran 6 tests in 0.012s -32: -32: OK -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing reading existing pickle file (v2). -37: [05:51:05] Conflicting single bond directions around double bond at index 2. -37: [05:51:05] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [05:51:05] Conflicting single bond directions around double bond at index 4. -37: [05:51:05] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [05:51:05] Conflicting single bond directions around double bond at index 15. -37: [05:51:05] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [05:51:05] Conflicting single bond directions around double bond at index 2. -37: [05:51:05] BondStereo set to STEREONONE and single bond directions set to NONE. -37: [05:51:05] Conflicting single bond directions around double bond at index 1. -37: [05:51:05] BondStereo set to STEREONONE and single bond directions set to NONE. -37: -------------------------------------------------- - 33/235 Test #37: graphmoltestChirality .................. Passed 0.22 sec - 34/235 Test #44: molBundleTest .......................... Passed 0.07 sec -test 45 - Start 45: testSGroup - -45: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup -45: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -test 46 - Start 46: test-valgrind - -46: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind -46: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing combining molecules using pickles. +36: [15:23:04] Explicit valence for atom # 1 C, 5, is greater than permitted +36: [15:23:04] Explicit valence for atom # 1 C, 5, is greater than permitted +36: [15:23:04] Explicit valence for atom # 1 Si, 7, is greater than permitted +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.068s +2: +2: OK +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing reading existing pickle file (v2). +37: [15:23:04] Conflicting single bond directions around double bond at index 2. +37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [15:23:04] Conflicting single bond directions around double bond at index 4. +37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [15:23:04] Conflicting single bond directions around double bond at index 15. +37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [15:23:04] Conflicting single bond directions around double bond at index 2. +37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. +37: [15:23:04] Conflicting single bond directions around double bond at index 1. +37: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. + 29/235 Test #40: graphmolIterTest ....................... Passed 0.09 sec +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing combining molecules using pickles. 38: Atoms: 38: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 38: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: SP3 @@ -16829,46 +16809,56 @@ 38: 4 4->5 order: 1 38: 5 5->6 order: 1 38: 6 6->3 order: 1 -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing Issue164: Roundtrip Pickle Failure. -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing Issue219: Pickle Failure with Conformations. -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing Issue220: Pickle problems with bond stereochemistry. -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing query serialization. -36: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -30: ...[05:51:05] Molecule does not have explicit Hs. Consider calling AddHs() - 35/235 Test #32: pyDistGeom ............................. Passed 0.36 sec -test 47 - Start 47: graphmolTestsCatch +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing Issue164: Roundtrip Pickle Failure. +test 41 + Start 41: hanoiTest -47: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -38: [05:51:05] C=[$(C=O)] -38: [05:51:05] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing radical handling in pickles. -38: [05:51:05] done -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing sf.net issue 2788233. -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing sf.net issue 3202580. +41: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest +41: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing Issue219: Pickle Failure with Conformations. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing Issue220: Pickle problems with bond stereochemistry. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing query serialization. +37: -------------------------------------------------- + 30/235 Test #37: graphmoltestChirality .................. Passed 0.24 sec +test 42 + Start 42: graphmolMemTest1 + +42: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 +42: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 +32: ...... +32: ---------------------------------------------------------------------- +32: Ran 6 tests in 0.025s +32: +32: OK +38: [15:23:04] C=[$(C=O)] +38: [15:23:04] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing radical handling in pickles. +38: [15:23:04] done +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing sf.net issue 2788233. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing sf.net issue 3202580. 38: mass! 13.0034 -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing sf.net issue 3316407. -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing sf.net issue 3496759. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing sf.net issue 3316407. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing sf.net issue 3496759. 38: smi match: *C *C 38: smi match: **=* **=* 38: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -16900,8 +16890,14 @@ 38: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC 38: smi match: N#CN=N N#CN=N 38: smi match: N=NCC=O N=NCC=O + 31/235 Test #1: testCoordGen ........................... Passed 2.34 sec +test 43 + Start 43: resMolSupplierTest + +43: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest +43: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 38: smi match: CCCCCCC CCCCCCC -36: [05:51:05] non-ring atom 0 marked aromatic 38: smi match: OCCOCCO OCCOCCO 38: smi match: SS SS 38: smi match: [SH] [SH] @@ -16928,16 +16924,10 @@ 38: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 38: smi match: N~NC=O N~NC=O 38: smi match: *=N~C *=N~C +41: [15:23:04] Testing the hanoi sort +41: [15:23:04] populating vectors 38: smi match: CO*(=O)=O CO*(=O)=O 38: smi match: * * - 36/235 Test #46: test-valgrind .......................... Passed 0.04 sec -test 48 - Start 48: graphmolOrganometallicsCatch - -48: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -48: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -36: [05:51:05] non-ring atom 0 marked aromatic 38: smi match: * * 38: smi match: *C=C *C=C 38: smi match: N#CS N#CS @@ -16977,13 +16967,6 @@ 38: smi match: C=CC=S C=CC=S 38: smi match: C=CC(=S)S C=CC(=S)S 38: smi match: *C=C(*)C=C *C=C(*)C=C -36: [05:51:05] Conflicting single bond directions around double bond at index 17. -36: [05:51:05] BondStereo set to STEREONONE and single bond directions set to NONE. -47: Randomness seeded to: 495557589 -47: [05:51:05] WARNING: not removing hydrogen atom without neighbors -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 38: smi match: C=CC=N C=CC=N 38: smi match: *N(*)C=C *N(*)C=C 38: smi match: C=CN(=O)=O C=CN(=O)=O @@ -17024,57 +17007,20 @@ 38: smi match: NOC(=O)O NOC(=O)O 38: smi match: *C(O)=S *C(O)=S 38: smi match: C=CO C=CO + 32/235 Test #42: graphmolMemTest1 ....................... Passed 0.04 sec +test 44 + Start 44: molBundleTest + +44: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest +44: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 38: smi match: ON=CC=NO ON=CC=NO 38: smi match: *C[SH](=O)=O *C[SH](=O)=O 38: smi match: OS(=O)=O OS(=O)=O 38: smi match: N#CS N#CS 38: smi match: C=C(S)S C=C(S)S -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -36: starting ring finding - 37/235 Test #45: testSGroup ............................. Passed 0.08 sec -36: done -test 49 - Start 49: graphmolSGroupCatch - -49: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch -49: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 -36: starting ring finding -36: done -36: starting ring finding -36: done -36: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -36: starting sanitization -47: [05:51:05] Explicit valence for atom # 1 N, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 N, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 N, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 N, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 2 O, 3, is greater than permitted -47: [05:51:05] Explicit valence for atom # 2 O, 3, is greater than permitted -47: [05:51:05] non-ring atom 2 marked aromatic -47: [05:51:05] non-ring atom 2 marked aromatic -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 1 2 3 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 1 2 3 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 -47: [05:51:05] Explicit valence for atom # 1 O, 3, is greater than permitted -47: [05:51:05] Explicit valence for atom # 4 F, 2, is greater than permitted -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 -47: [05:51:05] Explicit valence for atom # 1 C, 5, is greater than permitted -47: [05:51:05] WARNING: not removing hydrogen atom with dummy atom neighbors -47: [05:51:05] WARNING: not removing hydrogen atom with dummy atom neighbors -47: [05:51:05] WARNING: not removing hydrogen atom with wedged bond -47: [05:51:05] WARNING: not removing hydrogen atom without neighbors -47: [05:51:05] WARNING: not removing hydrogen atom without neighbors -47: [05:51:05] WARNING: not removing hydrogen atom without neighbors -47: [05:51:05] WARNING: not removing hydrogen atom without neighbors -47: [05:51:05] Unreasonable formal charge on atom # 0. -47: [05:51:05] -47: -47: **** 38: smi match: N=C(N)S N=C(N)S 38: smi match: N=C(S)S N=C(S)S 38: smi match: NC(=S)S NC(=S)S @@ -17120,6 +17066,381 @@ 38: smi match: N=CC=NO N=CC=NO 38: smi match: N#CCC#N N#CCC#N 38: smi match: CON=O CON=O +38: smi match: C=CN C=CN +38: smi match: C=N[SH](=O)=O C=N[SH](=O)=O +38: smi match: NN=O NN=O +38: smi match: NC(=O)S NC(=O)S +38: smi match: N#CS N#CS +38: smi match: NC(=O)C(N)=O NC(=O)C(N)=O +38: smi match: c=N c=N +38: smi match: C1COCO1 C1COCO1 +38: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O +38: smi match: O=CC=O O=CC=O +38: smi match: O=CNOC=O O=CNOC=O +38: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 +38: smi match: ONO ONO +38: smi match: ON(~O)~O ON(~O)~O +38: smi match: OC1COC(O)C1 OC1COC(O)C1 +38: smi match: OC1CCOC1O OC1CCOC1O +38: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 +38: smi match: N=[N+]=N N=[N+]=N +38: smi match: N#CN N#CN +38: smi match: C=NN=C C=NN=C +38: smi match: *CCN(C)C *CCN(C)C +38: smi match: CNN CNN +38: smi match: *CC *CC +38: smi match: OCS OCS +38: smi match: C1NO1 C1NO1 +38: smi match: COS(C)(=O)=O COS(C)(=O)=O +38: smi match: C1CO1 C1CO1 +38: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 +38: smi match: *C(*)=C *C(*)=C +38: smi match: N#[NH+] N#[NH+] +38: smi match: C#NO C#NO +38: smi match: OOO OOO +38: smi match: OO OO +38: smi match: O~Cl(~O)~O O~Cl(~O)~O +38: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O +38: smi match: [OH]~C(~O)~O [OH]~C(~O)~O +38: smi match: *N *N +38: smi match: *P *P +38: smi match: *S *S +38: smi match: *C(*)(*)C=C *C(*)(*)C=C +38: smi match: *C(*)(*)C=C *C(*)(*)C=C +38: smi match: *C(*)C=C *C(*)C=C +38: smi match: *CC=C *CC=C +38: smi match: CN=C=O CN=C=O +38: smi match: CN=C=S CN=C=S +38: smi match: *C=O *C=O +38: smi match: N=N N=N +38: smi match: SS SS +38: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 +38: smi match: CSC(C)=N CSC(C)=N +38: smi match: COC(C)=N COC(C)=N +38: smi match: C=C=C C=C=C +38: smi match: *C(=O)OC=O *C(=O)OC=O +38: smi match: C=CC#N C=CC#N +38: smi match: C=CC=O C=CC=O +38: smi match: CC=CC(C)=O CC=CC(C)=O +38: smi match: CC=CC(=O)OCC CC=CC(=O)OCC +38: smi match: C#CC#N C#CC#N +38: smi match: C#CC=O C#CC=O +38: smi match: C#CC(=O)OCC C#CC(=O)OCC +38: smi match: C#CC=O C#CC=O +38: smi match: *C(=O)C#C *C(=O)C#C +38: smi match: C=CC=O C=CC=O +38: smi match: *C(*)(*)O *C(*)(*)O +38: smi match: COS(O)(=O)=O COS(O)(=O)=O +38: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] +38: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] +38: smi match: *C(*)(*)C=O *C(*)(*)C=O +38: smi match: *C(*)(*)C=O *C(*)(*)C=O +38: smi match: *C(*)C=O *C(*)C=O +38: smi match: *CC=O *CC=O +38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O +38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O +38: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O +38: smi match: *C[SH](=O)=O *C[SH](=O)=O +38: smi match: * * +38: smi match: *1CC1 *1CC1 +38: smi match: O=COC=O O=COC=O +38: smi match: N=C=O N=C=O +38: smi match: N=C=S N=C=S +38: smi match: O~O O~O +38: smi match: N~[SiH4] N~[SiH4] +38: smi match: *P *P +38: smi match: C=N=N C=N=N +38: smi match: *N#[NH+] *N#[NH+] +38: smi match: *S* *S* +38: smi match: ** ** +38: smi match: *CC* *CC* +38: smi match: *O[SiH3] *O[SiH3] +38: smi match: *OS(*)~O *OS(*)~O +38: smi match: N~N~O N~N~O +38: smi match: *N(~O)(~O)~O *N(~O)(~O)~O +38: smi match: *[N+](=C)[O-] *[N+](=C)[O-] +38: smi match: * * +38: smi match: *C(*)NCN(*)* *C(*)NCN(*)* +38: smi match: *OCC#N *OCC#N +38: smi match: **C=C **C=C +38: smi match: C=C[O-] C=C[O-] +38: smi match: C=CO C=CO +38: smi match: * * +38: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O +38: smi match: O=COn1ccnc1 O=COn1ccnc1 +38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +38: smi match: CC(C)(C)S CC(C)(C)S +38: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C +38: smi match: [CH]=O [CH]=O +38: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C +38: smi match: SS SS +38: smi match: [SH] [SH] +38: smi match: *C* *C* +38: smi match: * * +38: smi match: C[nH3+] C[nH3+] +38: smi match: cC(=N)[NH2] cC(=N)[NH2] +38: smi match: O=CN[OH] O=CN[OH] +38: smi match: NN NN +38: smi match: * * +38: smi match: *OP(=O)O* *OP(=O)O* +38: smi match: * * +38: smi match: * * +38: smi match: * * + 33/235 Test #44: molBundleTest .......................... Passed 0.06 sec +test 45 + Start 45: testSGroup + +45: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup +45: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 +38: smi match: *N=C(*)* *N=C(*)* +38: smi match: *C(*)(*)C=O *C(*)(*)C=O +38: smi match: CSC=O CSC=O +38: smi match: * * +38: smi match: O=CCl O=CCl +38: smi match: *** *** +38: smi match: *C=O *C=O +38: smi match: C[OH] C[OH] +38: smi match: C[OH] C[OH] +38: smi match: C[OH] C[OH] +38: smi match: C[OH] C[OH] +38: smi match: C[CH]=O C[CH]=O +38: smi match: *=* *=* +38: smi match: *C *C +38: smi match: C#C C#C +38: smi match: *[CH]C=C *[CH]C=C +38: smi match: cCC(=O)[OH] cCC(=O)[OH] +38: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] +38: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] +38: smi match: C=CC(=O)[OH] C=CC(=O)[OH] +38: smi match: N#CC(=O)[OH] N#CC(=O)[OH] +38: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O +38: smi match: *N(*)C*=O *N(*)C*=O +38: smi match: O=*C[OH] O=*C[OH] +38: smi match: *=C*=O *=C*=O +38: smi match: *=CC#N *=CC#N +38: smi match: *C[OH] *C[OH] +38: smi match: ** ** +38: smi match: *C[OH] *C[OH] +38: smi match: *C(*)=O *C(*)=O +38: smi match: * * +38: smi match: *CC(=O)[OH] *CC(=O)[OH] +38: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O +38: smi match: *c *c +38: smi match: CN(C)c CN(C)c +38: smi match: c c +38: smi match: *c *c +38: smi match: *c *c +38: smi match: **:*cF **:*cF +38: smi match: cB([OH])[OH] cB([OH])[OH] +38: smi match: N~N~N N~N~N +38: smi match: *N=N* *N=N* +38: smi match: *CC[OH] *CC[OH] +36: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +38: smi match: *CC[OH] *CC[OH] +38: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] +38: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +38: smi match: *CCC(=O)[OH] *CCC(=O)[OH] +38: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] +38: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O +38: smi match: *OC(*)=O *OC(*)=O +38: smi match: *C(=O)[OH] *C(=O)[OH] +38: smi match: O=C[OH] O=C[OH] +38: smi match: *OC(=O)O* *OC(=O)O* +38: smi match: * * +38: smi match: *OC(=O)Cl *OC(=O)Cl +38: smi match: *C#N *C#N +38: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +38: smi match: SS SS +38: smi match: * * +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: *=* *=* +38: smi match: C1CO1 C1CO1 +38: smi match: *OC(*)=O *OC(*)=O +38: smi match: * * +38: smi match: *O*[OH] *O*[OH] +38: smi match: COC(C)(C)O COC(C)(C)O +38: smi match: *[OH] *[OH] +38: smi match: ** ** +38: smi match: C=N[NH2] C=N[NH2] +38: smi match: C=NC=O C=NC=O +38: smi match: * * +38: smi match: C#NC C#NC +38: smi match: CN=C=O CN=C=O +38: smi match: CN=C=S CN=C=S +38: smi match: *OC(*)(*)O* *OC(*)(*)O* +38: smi match: *C(*)=O *C(*)=O +38: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C +38: smi match: *~*=O *~*=O +38: smi match: *~*=O *~*=O +38: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] +38: smi match: * * +38: smi match: *C#N *C#N +38: smi match: *N(=O)~O *N(=O)~O +38: smi match: N N +38: smi match: OC(=O)C(O)=O OC(=O)C(O)=O +38: smi match: C=NO C=NO +38: smi match: O~O O~O +38: smi match: c[OH] c[OH] +38: smi match: O=P(~[OH])~O O=P(~[OH])~O +38: smi match: CO~P(=O)~O CO~P(=O)~O +38: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O +38: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O +38: smi match: O=P(~O)~O O=P(~O)~O +38: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O +38: smi match: C[NH2] C[NH2] +38: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 +38: smi match: * * +38: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 +38: smi match: CS(C)~O CS(C)~O +38: smi match: CS(C)(~O)~O CS(C)(~O)~O +38: smi match: CS(N)(~O)~O CS(N)(~O)~O +38: smi match: CS([OH])(~O)~O CS([OH])(~O)~O +38: smi match: COS(C)(~O)~O COS(C)(~O)~O +38: smi match: *S(C)(~O)~O *S(C)(~O)~O +38: smi match: CN(C)C CN(C)C +38: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 +38: smi match: *C(*)=S *C(*)=S +38: smi match: *OC(*)=S *OC(*)=S +38: smi match: * * +38: smi match: C[SH] C[SH] +38: smi match: c[SH] c[SH] +38: smi match: NC(N)=S NC(N)=S +38: smi match: * * +38: smi match: ***** ***** +38: smi match: NC(N)=O NC(N)=O +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing sf.net issue 280. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing sf.net issue 285. +38: [15:23:04] done +38: [15:23:04] done +38: [15:23:04] done +38: [15:23:04] done +38: [15:23:04] done +38: [15:23:04] done +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing Github2441: Add RDProps interface to Conformers. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing Issue2510: Pickle Confs as double. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing loading pickled mols with conformers +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing conformer reading/writing options +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing property reading options +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing property reading options +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing boost::serialization integration + 34/235 Test #32: pyDistGeom ............................. Passed 0.53 sec +test 46 + Start 46: test-valgrind + +46: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind +46: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 +38: [15:23:04] done +38: [15:23:04] ------------------------------------- +38: [15:23:04] Testing github issue 6036 + 35/235 Test #38: graphmoltestPickler .................... Passed 0.38 sec +test 47 + Start 47: graphmolTestsCatch + +47: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +36: [15:23:04] non-ring atom 0 marked aromatic +36: [15:23:04] non-ring atom 0 marked aromatic +36: [15:23:04] Conflicting single bond directions around double bond at index 17. +36: [15:23:04] BondStereo set to STEREONONE and single bond directions set to NONE. + 36/235 Test #2: pyCoordGen ............................. Passed 2.49 sec +36: starting ring finding +test 48 + Start 48: graphmolOrganometallicsCatch + +48: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +48: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +36: done +36: starting ring finding +36: done +36: starting ring finding +36: done +36: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +36: starting sanitization + 37/235 Test #46: test-valgrind .......................... Passed 0.06 sec +test 49 + Start 49: graphmolSGroupCatch + +49: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch +49: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 +36: done +36: starting sanitization +36: done +47: Randomness seeded to: 1355612572 +47: [15:23:05] WARNING: not removing hydrogen atom without neighbors +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [15:23:05] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 N, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 N, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 2 O, 3, is greater than permitted +47: [15:23:05] Explicit valence for atom # 2 O, 3, is greater than permitted +47: [15:23:05] non-ring atom 2 marked aromatic +47: [15:23:05] non-ring atom 2 marked aromatic +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 1 2 3 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 1 2 3 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 +47: [15:23:05] Explicit valence for atom # 1 O, 3, is greater than permitted +47: [15:23:05] Explicit valence for atom # 4 F, 2, is greater than permitted +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 +47: [15:23:05] Explicit valence for atom # 1 C, 5, is greater than permitted +47: [15:23:05] WARNING: not removing hydrogen atom with dummy atom neighbors +47: [15:23:05] WARNING: not removing hydrogen atom with dummy atom neighbors +47: [15:23:05] WARNING: not removing hydrogen atom with wedged bond +47: [15:23:05] WARNING: not removing hydrogen atom without neighbors +47: [15:23:05] WARNING: not removing hydrogen atom without neighbors + 38/235 Test #45: testSGroup ............................. Passed 0.14 sec +test 50 + Start 50: graphmolAdjustQueryCatch + +50: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +50: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 +47: [15:23:05] WARNING: not removing hydrogen atom without neighbors +47: [15:23:05] WARNING: not removing hydrogen atom without neighbors +47: [15:23:05] Unreasonable formal charge on atom # 0. +36: starting ring finding +36: done +36: starting ring finding +36: done +36: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 +47: [15:23:05] +47: +47: **** 47: Pre-condition Violation 47: no atom 47: Violation occurred on line 181 in file ./Code/GraphMol/ROMol.cpp @@ -17129,20 +17450,22 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5AC84 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BAC84 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +36: [15:23:05] WARNING: not removing hydrogen atom with dummy atom neighbors +30: ...[15:23:05] Molecule does not have explicit Hs. Consider calling AddHs() +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17154,20 +17477,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5ACF8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BACF8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17179,20 +17502,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomDegree(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5AD78 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BAD78 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17204,20 +17527,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5AE40 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BAE40 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17229,20 +17552,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5AEB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BAEB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17254,20 +17577,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomNeighbors(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5AF3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BAF3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17279,20 +17602,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5B650 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BB650 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17304,20 +17627,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5B06C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BB06C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17329,20 +17652,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::getAtomBonds(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5B0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BB0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17354,20 +17677,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5B634 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BB634 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17379,20 +17702,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5B2E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BB2E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17404,24 +17727,24 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::ROMol::addBond(RDKit::Bond*, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D5B614 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE40BB614 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [05:51:05] WARNING: not removing hydrogen atom without neighbors -47: [05:51:05] Explicit valence for atom # 1 F greater than permitted -47: [05:51:05] +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [15:23:05] WARNING: not removing hydrogen atom without neighbors +47: [15:23:05] Explicit valence for atom # 1 F greater than permitted +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17433,20 +17756,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Atom::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D0B0EC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE406B0EC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17458,20 +17781,20 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Atom::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D0B178 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE406B178 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** 47: Pre-condition Violation @@ -17483,63 +17806,22 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Bond::setQuery(Queries::Query*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D0AD3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE406AD3C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] +47: [15:23:05] 47: 47: **** -38: smi match: C=CN C=CN -38: smi match: C=N[SH](=O)=O C=N[SH](=O)=O -38: smi match: NN=O NN=O -38: smi match: NC(=O)S NC(=O)S -38: smi match: N#CS N#CS -38: smi match: NC(=O)C(N)=O NC(=O)C(N)=O -38: smi match: c=N c=N -38: smi match: C1COCO1 C1COCO1 -38: smi match: C=NN[SH](=O)=O C=NN[SH](=O)=O -38: smi match: O=CC=O O=CC=O -38: smi match: O=CNOC=O O=CNOC=O -38: smi match: O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 -38: smi match: ONO ONO -38: smi match: ON(~O)~O ON(~O)~O -38: smi match: OC1COC(O)C1 OC1COC(O)C1 -38: smi match: OC1CCOC1O OC1CCOC1O -38: smi match: OC1CCOC(O)C1 OC1CCOC(O)C1 -38: smi match: N=[N+]=N N=[N+]=N -38: smi match: N#CN N#CN -38: smi match: C=NN=C C=NN=C -38: smi match: *CCN(C)C *CCN(C)C -38: smi match: CNN CNN -38: smi match: *CC *CC -38: smi match: OCS OCS -38: smi match: C1NO1 C1NO1 -38: smi match: COS(C)(=O)=O COS(C)(=O)=O -38: smi match: C1CO1 C1CO1 -38: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 -38: smi match: *C(*)=C *C(*)=C -38: smi match: N#[NH+] N#[NH+] -38: smi match: C#NO C#NO -38: smi match: OOO OOO -38: smi match: OO OO -38: smi match: O~Cl(~O)~O O~Cl(~O)~O -38: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O -38: smi match: [OH]~C(~O)~O [OH]~C(~O)~O -38: smi match: *N *N -38: smi match: *P *P -38: smi match: *S *S -38: smi match: *C(*)(*)C=C *C(*)(*)C=C -38: smi match: *C(*)(*)C=C *C(*)(*)C=C 47: Pre-condition Violation 47: plain bonds have no query 47: Violation occurred on line 228 in file ./Code/GraphMol/Bond.cpp @@ -17549,426 +17831,202 @@ 47: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 47: 2# RDKit::Bond::expandQuery(Queries::Query*, Queries::CompositeQueryType, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -47: 3# 0x0000AAAAB6D0ADC8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 4# 0x0000AAAAB6DA4E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 5# 0x0000AAAAB6DA5820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 6# 0x0000AAAAB6DA5C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 7# 0x0000AAAAB6D7A038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 8# 0x0000AAAAB6D7A584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 9# 0x0000AAAAB6CFE030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -47: 10# 0x0000FFFFB047229C in /lib/aarch64-linux-gnu/libc.so.6 +47: 3# 0x0000AAAAE406ADC8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 4# 0x0000AAAAE4104E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 5# 0x0000AAAAE4105820 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 6# 0x0000AAAAE4105C54 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 7# 0x0000AAAAE40DA038 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 8# 0x0000AAAAE40DA584 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 9# 0x0000AAAAE405E030 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 10# 0x0000FFFF8FBA229C in /lib/aarch64-linux-gnu/libc.so.6 47: 11# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -47: 12# 0x0000AAAAB6CFE0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +47: 12# 0x0000AAAAE405E0F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 47: ---------- 47: **** 47: -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -36: done -36: starting sanitization -47: [05:51:05] Unusual charge on atom 0 number of radical electrons set to zero -47: [05:51:05] Unusual charge on atom 0 number of radical electrons set to zero -47: [05:51:05] Unusual charge on atom 0 number of radical electrons set to zero -47: [05:51:05] non-ring atom 0 marked aromatic -47: [05:51:05] non-ring atom 0 marked aromatic -47: [05:51:05] Explicit valence for atom # 1 C, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 3 N, 4, is greater than permitted -47: [05:51:05] Explicit valence for atom # 15 C, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 11 C, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 9 C, 5, is greater than permitted -47: [05:51:05] Explicit valence for atom # 9 C, 6, is greater than permitted -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 7 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 3 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 3 7 -47: [05:51:05] Can't kekulize mol. Unkekulized atoms: 3 7 -38: smi match: *C(*)C=C *C(*)C=C -38: smi match: *CC=C *CC=C -38: smi match: CN=C=O CN=C=O -38: smi match: CN=C=S CN=C=S -38: smi match: *C=O *C=O -38: smi match: N=N N=N -38: smi match: SS SS -38: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 -38: smi match: CSC(C)=N CSC(C)=N -38: smi match: COC(C)=N COC(C)=N -38: smi match: C=C=C C=C=C -38: smi match: *C(=O)OC=O *C(=O)OC=O -38: smi match: C=CC#N C=CC#N -38: smi match: C=CC=O C=CC=O -38: smi match: CC=CC(C)=O CC=CC(C)=O -38: smi match: CC=CC(=O)OCC CC=CC(=O)OCC -38: smi match: C#CC#N C#CC#N -38: smi match: C#CC=O C#CC=O -38: smi match: C#CC(=O)OCC C#CC(=O)OCC -38: smi match: C#CC=O C#CC=O -38: smi match: *C(=O)C#C *C(=O)C#C -38: smi match: C=CC=O C=CC=O -38: smi match: *C(*)(*)O *C(*)(*)O -38: smi match: COS(O)(=O)=O COS(O)(=O)=O -38: smi match: CS(=O)(=O)[O-] CS(=O)(=O)[O-] -38: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] -38: smi match: *C(*)(*)C=O *C(*)(*)C=O -38: smi match: *C(*)(*)C=O *C(*)(*)C=O -38: smi match: *C(*)C=O *C(*)C=O -38: smi match: *CC=O *CC=O -36: done -38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O -38: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O -38: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O -38: smi match: *C[SH](=O)=O *C[SH](=O)=O -38: smi match: * * -38: smi match: *1CC1 *1CC1 -38: smi match: O=COC=O O=COC=O -38: smi match: N=C=O N=C=O -38: smi match: N=C=S N=C=S -38: smi match: O~O O~O -38: smi match: N~[SiH4] N~[SiH4] -38: smi match: *P *P -38: smi match: C=N=N C=N=N -38: smi match: *N#[NH+] *N#[NH+] -38: smi match: *S* *S* -38: smi match: ** ** -38: smi match: *CC* *CC* -38: smi match: *O[SiH3] *O[SiH3] -38: smi match: *OS(*)~O *OS(*)~O -38: smi match: N~N~O N~N~O -38: smi match: *N(~O)(~O)~O *N(~O)(~O)~O -38: smi match: *[N+](=C)[O-] *[N+](=C)[O-] -38: smi match: * * -38: smi match: *C(*)NCN(*)* *C(*)NCN(*)* -38: smi match: *OCC#N *OCC#N -38: smi match: **C=C **C=C -38: smi match: C=C[O-] C=C[O-] -38: smi match: C=CO C=CO -38: smi match: * * -38: smi match: O=CON1C(=O)CCC1=O O=CON1C(=O)CCC1=O -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -47: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -36: starting ring finding -36: done -36: starting ring finding -36: done -36: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -48: Randomness seeded to: 1828374614 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +36: ------------------------------- +36: [15:23:05] Explicit valence for atom # 0 N, 4, is greater than permitted +48: Randomness seeded to: 1685663689 48: =============================================================================== 48: All tests passed (62 assertions in 6 test cases) 48: -38: smi match: O=COn1ccnc1 O=COn1ccnc1 - 38/235 Test #48: graphmolOrganometallicsCatch ........... Passed 0.07 sec -38: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F -38: smi match: CC(C)(C)S CC(C)(C)S -test 50 - Start 50: graphmolAdjustQueryCatch - -50: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -50: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol -50: Test timeout computed to be: 1500 -38: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C -38: smi match: [CH]=O [CH]=O -38: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C -38: smi match: SS SS -38: smi match: [SH] [SH] -38: smi match: *C* *C* -38: smi match: * * -38: smi match: C[nH3+] C[nH3+] -38: smi match: cC(=N)[NH2] cC(=N)[NH2] -38: smi match: O=CN[OH] O=CN[OH] -38: smi match: NN NN -38: smi match: * * -38: smi match: *OP(=O)O* *OP(=O)O* -38: smi match: * * -38: smi match: * * -38: smi match: * * -38: smi match: *N=C(*)* *N=C(*)* -38: smi match: *C(*)(*)C=O *C(*)(*)C=O -38: smi match: CSC=O CSC=O -38: smi match: * * -38: smi match: O=CCl O=CCl -38: smi match: *** *** -38: smi match: *C=O *C=O -38: smi match: C[OH] C[OH] -38: smi match: C[OH] C[OH] -38: smi match: C[OH] C[OH] -38: smi match: C[OH] C[OH] -38: smi match: C[CH]=O C[CH]=O -38: smi match: *=* *=* -38: smi match: *C *C -38: smi match: C#C C#C -38: smi match: *[CH]C=C *[CH]C=C -38: smi match: cCC(=O)[OH] cCC(=O)[OH] -38: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] -38: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] -38: smi match: C=CC(=O)[OH] C=CC(=O)[OH] -38: smi match: N#CC(=O)[OH] N#CC(=O)[OH] -38: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O -38: smi match: *N(*)C*=O *N(*)C*=O -38: smi match: O=*C[OH] O=*C[OH] -38: smi match: *=C*=O *=C*=O -38: smi match: *=CC#N *=CC#N -38: smi match: *C[OH] *C[OH] -38: smi match: ** ** -38: smi match: *C[OH] *C[OH] -38: smi match: *C(*)=O *C(*)=O -49: Randomness seeded to: 1875042488 -49: =============================================================================== -49: All tests passed (136 assertions in 8 test cases) -49: - 39/235 Test #49: graphmolSGroupCatch .................... Passed 0.06 sec + 39/235 Test #48: graphmolOrganometallicsCatch ........... Passed 0.07 sec test 51 Start 51: chiralityTestsCatch 51: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 -41: [05:51:05] sorting (hanoi sort) vectors -36: [05:51:05] WARNING: not removing hydrogen atom with dummy atom neighbors -38: smi match: * * -38: smi match: *CC(=O)[OH] *CC(=O)[OH] -38: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O -38: smi match: *c *c -38: smi match: CN(C)c CN(C)c -38: smi match: c c -38: smi match: *c *c -38: smi match: *c *c -38: smi match: **:*cF **:*cF -38: smi match: cB([OH])[OH] cB([OH])[OH] -38: smi match: N~N~N N~N~N -38: smi match: *N=N* *N=N* -38: smi match: *CC[OH] *CC[OH] -38: smi match: *CC[OH] *CC[OH] -38: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -38: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] -38: smi match: *CCC(=O)[OH] *CCC(=O)[OH] -38: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -38: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O -38: smi match: *OC(*)=O *OC(*)=O -38: smi match: *C(=O)[OH] *C(=O)[OH] -38: smi match: O=C[OH] O=C[OH] -38: smi match: *OC(=O)O* *OC(=O)O* -38: smi match: * * -36: ------------------------------- -36: [05:51:05] Explicit valence for atom # 0 N, 4, is greater than permitted -38: smi match: *OC(=O)Cl *OC(=O)Cl -38: smi match: *C#N *C#N -38: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -38: smi match: SS SS -38: smi match: * * -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: *=* *=* -38: smi match: C1CO1 C1CO1 -38: smi match: *OC(*)=O *OC(*)=O -38: smi match: * * -38: smi match: *O*[OH] *O*[OH] -38: smi match: COC(C)(C)O COC(C)(C)O -38: smi match: *[OH] *[OH] -38: smi match: ** ** -38: smi match: C=N[NH2] C=N[NH2] -38: smi match: C=NC=O C=NC=O -47: [05:51:05] Explicit valence for atom # 1 O, 3, is greater than permitted -47: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -47: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -47: [05:51:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [05:51:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -38: smi match: * * -38: smi match: C#NC C#NC -38: smi match: CN=C=O CN=C=O -38: smi match: CN=C=S CN=C=S -38: smi match: *OC(*)(*)O* *OC(*)(*)O* -38: smi match: *C(*)=O *C(*)=O -38: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C -38: smi match: *~*=O *~*=O -38: smi match: *~*=O *~*=O -38: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] -38: smi match: * * -38: smi match: *C#N *C#N -38: smi match: *N(=O)~O *N(=O)~O -38: smi match: N N -38: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -38: smi match: C=NO C=NO -38: smi match: O~O O~O -38: smi match: c[OH] c[OH] -38: smi match: O=P(~[OH])~O O=P(~[OH])~O -38: smi match: CO~P(=O)~O CO~P(=O)~O -38: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O -38: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O -38: smi match: O=P(~O)~O O=P(~O)~O -38: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O -38: smi match: C[NH2] C[NH2] -38: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 -38: smi match: * * -38: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 -38: smi match: CS(C)~O CS(C)~O -38: smi match: CS(C)(~O)~O CS(C)(~O)~O -38: smi match: CS(N)(~O)~O CS(N)(~O)~O -38: smi match: CS([OH])(~O)~O CS([OH])(~O)~O -38: smi match: COS(C)(~O)~O COS(C)(~O)~O -38: smi match: *S(C)(~O)~O *S(C)(~O)~O -38: smi match: CN(C)C CN(C)C -38: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 -38: smi match: *C(*)=S *C(*)=S -36: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -36: [05:51:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -36: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -38: smi match: *OC(*)=S *OC(*)=S -36: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -36: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +36: [15:23:05] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +36: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +36: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 36: -38: smi match: * * -38: smi match: C[SH] C[SH] -38: smi match: c[SH] c[SH] -38: smi match: NC(N)=S NC(N)=S -38: smi match: * * -38: smi match: ***** ***** -38: smi match: NC(N)=O NC(N)=O -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing sf.net issue 280. -47: [05:51:05] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. -47: [05:51:05] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom -47: [05:51:05] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom -47: [05:51:05] non-ring atom 0 marked aromatic -36: [05:51:05] WARNING: not removing hydrogen atom with dummy atom neighbors -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing sf.net issue 285. -38: [05:51:05] done -38: [05:51:05] done -38: [05:51:05] done -38: [05:51:05] done -38: [05:51:05] done -38: [05:51:05] done -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing Github2441: Add RDProps interface to Conformers. -51: Randomness seeded to: 743628422 -51: [05:51:05] unable to set wavy bonds for double bonds: 3 -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing Issue2510: Pickle Confs as double. -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing loading pickled mols with conformers -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing conformer reading/writing options -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing property reading options -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing property reading options -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing boost::serialization integration -47: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -38: [05:51:05] done -38: [05:51:05] ------------------------------------- -38: [05:51:05] Testing github issue 6036 - 40/235 Test #38: graphmoltestPickler .................... Passed 0.41 sec +47: [15:23:05] Unusual charge on atom 0 number of radical electrons set to zero +47: [15:23:05] Unusual charge on atom 0 number of radical electrons set to zero +47: [15:23:05] Unusual charge on atom 0 number of radical electrons set to zero +47: [15:23:05] non-ring atom 0 marked aromatic +47: [15:23:05] non-ring atom 0 marked aromatic +47: [15:23:05] Explicit valence for atom # 1 C, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 3 N, 4, is greater than permitted +47: [15:23:05] Explicit valence for atom # 15 C, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 11 C, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 9 C, 5, is greater than permitted +47: [15:23:05] Explicit valence for atom # 9 C, 6, is greater than permitted +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 7 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 3 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 3 7 +47: [15:23:05] Can't kekulize mol. Unkekulized atoms: 3 7 +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +47: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +36: [15:23:05] WARNING: not removing hydrogen atom with dummy atom neighbors +49: Randomness seeded to: 2437238120 +49: =============================================================================== +49: All tests passed (136 assertions in 8 test cases) +49: + 40/235 Test #49: graphmolSGroupCatch .................... Passed 0.10 sec test 52 Start 52: canonTestsCatch 52: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 -51: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -51: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -47: [05:51:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -50: Randomness seeded to: 3302104999 +47: [15:23:05] Explicit valence for atom # 1 O, 3, is greater than permitted +47: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +47: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [15:23:05] Invalid value for molAttachPoint: 4 on atom 1. Not expanding this atttachment point. +47: [15:23:05] Invalid value for _fromAttachPoint: -1 on atom 0. Not collapsing this atom +47: [15:23:05] Invalid value for _fromAttachPoint: 4 on atom 0. Not collapsing this atom +41: [15:23:05] sorting (hanoi sort) vectors +51: Randomness seeded to: 2409308902 +50: Randomness seeded to: 1434556895 50: =============================================================================== 50: All tests passed (283 assertions in 11 test cases) 50: - 41/235 Test #50: graphmolAdjustQueryCatch ............... Passed 0.10 sec + 41/235 Test #50: graphmolAdjustQueryCatch ............... Passed 0.14 sec test 53 Start 53: moliteratorTestsCatch 53: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 53: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 53: Test timeout computed to be: 1500 -51: [05:51:05] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -51: [05:51:05] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -51: [05:51:05] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -47: [05:51:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +51: [15:23:05] unable to set wavy bonds for double bonds: 3 +47: [15:23:05] non-ring atom 0 marked aromatic +47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +51: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +51: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +51: [15:23:05] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +51: [15:23:05] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +51: [15:23:05] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 51: =============================================================================== 51: All tests passed (2267 assertions in 79 test cases) 51: - 42/235 Test #51: chiralityTestsCatch .................... Passed 0.11 sec + 42/235 Test #51: chiralityTestsCatch .................... Passed 0.23 sec test 54 Start 54: queryTestsCatch 54: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch 54: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 54: Test timeout computed to be: 1500 -53: Randomness seeded to: 1023453956 +47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [15:23:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +30: ......[15:23:05] Molecule does not have explicit Hs. Consider calling AddHs() +36: [15:23:05] Maximum BFS search size exceeded. +36: This is likely due to a highly symmetric fused ring system. +53: Randomness seeded to: 317281418 53: =============================================================================== 53: All tests passed (14 assertions in 4 test cases) 53: -47: [05:51:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -47: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored - 43/235 Test #53: moliteratorTestsCatch .................. Passed 0.05 sec + 43/235 Test #53: moliteratorTestsCatch .................. Passed 0.27 sec test 55 Start 55: molbundleTestsCatch 55: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/molbundleTestsCatch 55: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 55: Test timeout computed to be: 1500 -54: Randomness seeded to: 3773387734 -54: =============================================================================== -54: All tests passed (10 assertions in 1 test case) -54: - 44/235 Test #54: queryTestsCatch ........................ Passed 0.04 sec +47: [15:23:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +47: [15:23:05] Explicit valence for atom # 0 Al, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 Al, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 Si, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 Si, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 P, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 P, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 P, 7, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 P, 7, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 As, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 As, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 As, 7, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 As, 7, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 Sb, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 Sb, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 Sb, 7, is greater than permitted +47: [15:23:05] Explicit valence for atom # 0 Sb, 7, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 Bi, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 Bi, 6, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 Bi, 8, is greater than permitted +47: [15:23:05] Explicit valence for atom # 1 Bi, 8, is greater than permitted +47: =============================================================================== +47: All tests passed (4464 assertions in 106 test cases) +47: + 44/235 Test #47: graphmolTestsCatch ..................... Passed 0.50 sec test 56 Start 56: pickleTestsCatch 56: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/pickleTestsCatch 56: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 56: Test timeout computed to be: 1500 -47: [05:51:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -30: ......[05:51:05] Molecule does not have explicit Hs. Consider calling AddHs() -55: Randomness seeded to: 3939490711 -55: =============================================================================== -55: All tests passed (6 assertions in 1 test case) -55: - 45/235 Test #55: molbundleTestsCatch .................... Passed 0.03 sec +30: ... +30: ---------------------------------------------------------------------- +30: Ran 12 tests in 0.729s +30: +30: OK +56: Randomness seeded to: 4178049553 +56: =============================================================================== +56: All tests passed (45 assertions in 4 test cases) +56: + 45/235 Test #56: pickleTestsCatch ....................... Passed 0.11 sec test 57 Start 57: tableTestsCatch 57: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/tableTestsCatch 57: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 57: Test timeout computed to be: 1500 -47: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [05:51:05] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -47: [05:51:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -56: Randomness seeded to: 4076843868 -56: =============================================================================== -56: All tests passed (45 assertions in 4 test cases) -56: - 46/235 Test #56: pickleTestsCatch ....................... Passed 0.06 sec +54: Randomness seeded to: 217692736 +54: =============================================================================== +54: All tests passed (10 assertions in 1 test case) +54: + 46/235 Test #54: queryTestsCatch ........................ Passed 0.36 sec test 58 Start 58: molopsTestsCatch 58: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/molopsTestsCatch 58: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol 58: Test timeout computed to be: 1500 -58: Randomness seeded to: 1273288298 +58: Randomness seeded to: 1260422142 58: =============================================================================== 58: All tests passed (79 assertions in 6 test cases) 58: @@ -17979,227 +18037,205 @@ 59: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 59: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] WARNING: not removing hydrogen atom without neighbors -59: [05:51:05] Invalid chiral specification on atom 0 -59: [05:51:05] Invalid chiral specification on atom 0 -59: [05:51:05] Invalid chiral specification on atom 0 -59: [05:51:05] Invalid chiral specification on atom 0 -59: [05:51:05] Invalid chiral specification on atom 0 -47: [05:51:05] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -47: [05:51:05] Explicit valence for atom # 0 Al, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 Al, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 Si, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 Si, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 P, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 P, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 P, 7, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 P, 7, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 As, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 As, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 As, 7, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 As, 7, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 Sb, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 Sb, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 Sb, 7, is greater than permitted -47: [05:51:05] Explicit valence for atom # 0 Sb, 7, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 Bi, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 Bi, 6, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 Bi, 8, is greater than permitted -47: [05:51:05] Explicit valence for atom # 1 Bi, 8, is greater than permitted -47: =============================================================================== -47: All tests passed (4464 assertions in 106 test cases) -47: -59: [05:51:05] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -59: [05:51:05] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' - 48/235 Test #47: graphmolTestsCatch ..................... Passed 0.46 sec +36: [15:23:05] Maximum BFS search size exceeded. +36: This is likely due to a highly symmetric fused ring system. + 48/235 Test #30: pyForceFieldConstraints ................ Passed 1.44 sec test 60 Start 60: smiTest2 60: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 60: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 60: Test timeout computed to be: 1500 -30: ... -30: ---------------------------------------------------------------------- -30: Ran 12 tests in 0.566s -30: -30: OK -60: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -60: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -60: [05:51:05] SMILES Parse Error: syntax error while parsing: - -60: [05:51:05] SMILES Parse Error: check for mistakes around position 1: -60: [05:51:05] - -60: [05:51:05] ^ -60: [05:51:05] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -60: [05:51:05] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -60: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -60: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -60: [05:51:05] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -60: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -60: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -60: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -60: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -60: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -60: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -60: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 49/235 Test #60: smiTest2 ............................... Passed 0.02 sec +36: F/C=C/Cl +36: [H]/C(F)=C(/[H])Cl +36: F/C=C/Cl +36: F/C=C/Cl +36: C/C(F)=C(/C)Cl +36: [15:23:05] ----------------------- +36: Testing isRingFused +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors + 49/235 Test #36: graphmolMolOpsTest ..................... Passed 1.30 sec test 61 Start 61: cxsmilesTest 61: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 61: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 61: Test timeout computed to be: 1500 -57: Randomness seeded to: 2729592688 -57: =============================================================================== -57: All tests passed (7 assertions in 2 test cases) -57: - 50/235 Test #57: tableTestsCatch ........................ Passed 0.24 sec +60: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +60: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +60: [15:23:05] SMILES Parse Error: syntax error while parsing: - +60: [15:23:05] SMILES Parse Error: check for mistakes around position 1: +60: [15:23:05] - +60: [15:23:05] ^ +60: [15:23:05] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +60: [15:23:05] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +60: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +60: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +60: [15:23:05] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +60: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' +59: [15:23:05] WARNING: not removing hydrogen atom without neighbors +59: [15:23:05] Invalid chiral specification on atom 0 +59: [15:23:05] Invalid chiral specification on atom 0 +59: [15:23:05] Invalid chiral specification on atom 0 +59: [15:23:05] Invalid chiral specification on atom 0 +59: [15:23:05] Invalid chiral specification on atom 0 + 50/235 Test #60: smiTest2 ............................... Passed 0.03 sec test 62 Start 62: smaTest1 62: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 62: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 62: Test timeout computed to be: 1500 -59: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -59: smi: ClC1CCCCC1 -59: smi: ClC1CCCCC1 -59: smi: ClC1CCCCC1Br -59: smi: c1ccccc1 -59: smi: c1ccncc1 -59: smi: c1cc[nH]c1 -59: smi: c1cc[nH]c1 -59: smi: c1cc[pH]c1 -59: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -59: [05:51:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. - 51/235 Test #30: pyForceFieldConstraints ................ Passed 1.01 sec +59: [15:23:05] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +59: [15:23:05] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +55: Randomness seeded to: 754812182 +55: =============================================================================== +55: All tests passed (6 assertions in 1 test case) +55: + 51/235 Test #55: molbundleTestsCatch .................... Passed 0.46 sec test 63 Start 63: smiTestCatch 63: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 63: Test timeout computed to be: 1500 -59: CbC(aC)aC -59: CaC(bC)aC -59: CbC(bC)aC -59: O.C -59: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -59: [05:51:05] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -59: [05:51:05] SMILES Parse Error: check for mistakes around position 4: -59: [05:51:05] c%()ccccc%() -59: [05:51:05] ~~~^ -59: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -59: [05:51:05] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -59: [05:51:05] SMILES Parse Error: check for mistakes around position 9: -59: [05:51:05] c%(100000)ccccc%(100000) -59: [05:51:05] ~~~~~~~~^ -59: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -59: [05:51:05] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -59: [05:51:05] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -59: [05:51:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [05:51:05] SMILES Parse Error: check for mistakes around position 14: -59: [05:51:05] COc(c1)cccc1C# -59: [05:51:05] ~~~~~~~~~~~~~^ -59: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [05:51:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [05:51:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [05:51:05] SMILES Parse Error: check for mistakes around position 14: -59: [05:51:05] COc(c1)cccc1C# -59: [05:51:05] ~~~~~~~~~~~~~^ -59: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [05:51:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [05:51:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [05:51:05] SMILES Parse Error: check for mistakes around position 14: -59: [05:51:05] COc(c1)cccc1C# -59: [05:51:05] ~~~~~~~~~~~~~^ -59: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: [05:51:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -59: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -59: C=c1s/c2n(c1=O)CCCCCCC\N=2 -59: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -59: [05:51:05] SMILES Parse Error: extra close parentheses while parsing: C) -59: [05:51:05] SMILES Parse Error: check for mistakes around position 2: -59: [05:51:05] C) -59: [05:51:05] ~^ -59: [05:51:05] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 52/235 Test #59: smiTest1 ............................... Passed 0.22 sec +57: Randomness seeded to: 3729418531 +57: =============================================================================== +57: All tests passed (7 assertions in 2 test cases) +57: +62: [15:23:05] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +62: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +62: [15:23:05] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +62: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +63: Randomness seeded to: 3100898158 +63: [15:23:05] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +63: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +63: [15:23:05] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' + 52/235 Test #57: tableTestsCatch ........................ Passed 0.36 sec test 64 Start 64: nontetrahedralCatch 64: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 64: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 64: Test timeout computed to be: 1500 -63: Randomness seeded to: 2542701798 -63: [05:51:05] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -63: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -63: [05:51:05] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -63: [05:51:05] SMARTS Parse Error: unclosed ring for input: 'C1C' -63: [05:51:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -63: [05:51:05] SMARTS Parse Error: syntax error while parsing: C)foo -63: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -63: [05:51:05] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -63: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -64: Randomness seeded to: 2315619163 -64: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -63: [05:51:05] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -64: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [05:51:05] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -62: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -62: [05:51:05] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -62: [05:51:05] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -64: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -64: [05:51:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -62: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -62: [05:51:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 53/235 Test #62: smaTest1 ............................... Passed 0.14 sec +63: [15:23:05] SMARTS Parse Error: unclosed ring for input: 'C1C' +63: [15:23:05] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +62: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +62: [15:23:05] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +63: [15:23:05] SMARTS Parse Error: syntax error while parsing: C)foo +63: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +63: [15:23:05] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +63: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +63: [15:23:05] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +59: --C1CCC2(CC1)CCCCC2CCC1CCCC1 + 53/235 Test #62: smaTest1 ............................... Passed 0.16 sec test 65 Start 65: v2smiTestCatch 65: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/v2smiTestCatch 65: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 65: Test timeout computed to be: 1500 -64: [05:51:05] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -64: =============================================================================== -64: All tests passed (308 assertions in 9 test cases) -64: - 54/235 Test #64: nontetrahedralCatch .................... Passed 0.09 sec +64: Randomness seeded to: 4082872462 +64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: smi: ClC1CCCCC1 +59: smi: ClC1CCCCC1 +59: smi: ClC1CCCCC1Br +59: smi: c1ccccc1 +59: smi: c1ccncc1 +59: smi: c1cc[nH]c1 +59: smi: c1cc[nH]c1 +59: smi: c1cc[pH]c1 +59: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +59: [15:23:05] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +59: CbC(aC)aC +59: CaC(bC)aC +59: CbC(bC)aC +59: O.C +59: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O +59: [15:23:05] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +59: [15:23:05] SMILES Parse Error: check for mistakes around position 4: +59: [15:23:05] c%()ccccc%() +59: [15:23:05] ~~~^ +59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +59: [15:23:05] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +59: [15:23:05] SMILES Parse Error: check for mistakes around position 9: +59: [15:23:05] c%(100000)ccccc%(100000) +59: [15:23:05] ~~~~~~~~^ +59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +59: [15:23:05] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +59: [15:23:05] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +59: [15:23:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [15:23:05] SMILES Parse Error: check for mistakes around position 14: +59: [15:23:05] COc(c1)cccc1C# +59: [15:23:05] ~~~~~~~~~~~~~^ +59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [15:23:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [15:23:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [15:23:05] SMILES Parse Error: check for mistakes around position 14: +59: [15:23:05] COc(c1)cccc1C# +59: [15:23:05] ~~~~~~~~~~~~~^ +59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [15:23:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [15:23:05] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [15:23:05] SMILES Parse Error: check for mistakes around position 14: +59: [15:23:05] COc(c1)cccc1C# +59: [15:23:05] ~~~~~~~~~~~~~^ +59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: [15:23:05] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +59: [15:23:05] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +59: C=c1s/c2n(c1=O)CCCCCCC\N=2 +59: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +59: [15:23:05] SMILES Parse Error: extra close parentheses while parsing: C) +59: [15:23:05] SMILES Parse Error: check for mistakes around position 2: +59: [15:23:05] C) +59: [15:23:05] ~^ +59: [15:23:05] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' +64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +64: [15:23:05] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 54/235 Test #59: smiTest1 ............................... Passed 0.28 sec test 66 Start 66: testDepictor 66: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor 66: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 66: Test timeout computed to be: 1500 -36: [05:51:06] Maximum BFS search size exceeded. -36: This is likely due to a highly symmetric fused ring system. -65: Randomness seeded to: 705740809 -65: =============================================================================== -65: All tests passed (14 assertions in 2 test cases) -65: - 55/235 Test #65: v2smiTestCatch ......................... Passed 0.04 sec +64: [15:23:06] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +64: =============================================================================== +64: All tests passed (308 assertions in 9 test cases) +64: + 55/235 Test #64: nontetrahedralCatch .................... Passed 0.07 sec test 67 Start 67: depictorCatch 67: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch 67: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 67: Test timeout computed to be: 1500 -63: [05:51:06] w block attempts to set wedging on bond 0 more than once. -63: [05:51:06] improperly formatted w block -63: [05:51:06] atom 3 is not associated with bond 1(1-2) in w block -63: [05:51:06] +63: [15:23:06] w block attempts to set wedging on bond 0 more than once. +63: [15:23:06] improperly formatted w block +63: [15:23:06] atom 3 is not associated with bond 1(1-2) in w block +63: [15:23:06] 63: 63: **** 63: Range Error @@ -18215,20 +18251,20 @@ 63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 7# 0x0000AAAAD6DE9B2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 8# 0x0000AAAAD6E3D50C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 9# 0x0000AAAAD6E3DEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 10# 0x0000AAAAD6E3E2F4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 11# 0x0000AAAAD6E126B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 12# 0x0000AAAAD6E12C04 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 13# 0x0000AAAAD6DA5810 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 14# 0x0000FFFFBD5F229C in /lib/aarch64-linux-gnu/libc.so.6 +63: 7# 0x0000AAAAD5BD9B2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 8# 0x0000AAAAD5C2D50C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 9# 0x0000AAAAD5C2DEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 10# 0x0000AAAAD5C2E2F4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 11# 0x0000AAAAD5C026B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 12# 0x0000AAAAD5C02C04 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 13# 0x0000AAAAD5B95810 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 14# 0x0000FFFFBC3B229C in /lib/aarch64-linux-gnu/libc.so.6 63: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -63: 16# 0x0000AAAAD6DA58F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 16# 0x0000AAAAD5B958F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: ---------- 63: **** 63: -63: [05:51:06] +63: [15:23:06] 63: 63: **** 63: Range Error @@ -18244,28 +18280,28 @@ 63: 4# RDKit::SmilesWrite::FragmentSmilesConstruct(RDKit::ROMol&, int, std::vector >&, std::vector > const&, RDKit::SmilesWriteParams const&, std::vector >&, std::vector >&, boost::dynamic_bitset > const*, boost::dynamic_bitset > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*, std::vector, std::allocator >, std::allocator, std::allocator > > > const*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 5# RDKit::SmilesWrite::detail::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 63: 6# RDKit::MolToSmiles[abi:cxx11](RDKit::ROMol const&, RDKit::SmilesWriteParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -63: 7# 0x0000AAAAD6DE9B2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 8# 0x0000AAAAD6E3D50C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 9# 0x0000AAAAD6E3DEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 10# 0x0000AAAAD6E3E2F4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 11# 0x0000AAAAD6E126B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 12# 0x0000AAAAD6E12C04 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 13# 0x0000AAAAD6DA5810 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch -63: 14# 0x0000FFFFBD5F229C in /lib/aarch64-linux-gnu/libc.so.6 +63: 7# 0x0000AAAAD5BD9B2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 8# 0x0000AAAAD5C2D50C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 9# 0x0000AAAAD5C2DEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 10# 0x0000AAAAD5C2E2F4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 11# 0x0000AAAAD5C026B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 12# 0x0000AAAAD5C02C04 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 13# 0x0000AAAAD5B95810 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 14# 0x0000FFFFBC3B229C in /lib/aarch64-linux-gnu/libc.so.6 63: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -63: 16# 0x0000AAAAD6DA58F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch +63: 16# 0x0000AAAAD5B958F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 63: ---------- 63: **** 63: -63: [05:51:06] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -63: [05:51:06] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' -63: [05:51:06] SMARTS Parse Error: syntax error while parsing: C1C)foo -63: [05:51:06] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' -63: [05:51:06] SMILES Parse Error: extra close parentheses while parsing: C1C)foo -63: [05:51:06] SMILES Parse Error: check for mistakes around position 4: -63: [05:51:06] C1C)foo -63: [05:51:06] ~~~^ -63: [05:51:06] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' +63: [15:23:06] SMARTS Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +63: [15:23:06] SMILES Parse Error: unclosed ring for input: 'C1.C2.C3.C4.C5' +63: [15:23:06] SMARTS Parse Error: syntax error while parsing: C1C)foo +63: [15:23:06] SMARTS Parse Error: Failed parsing SMARTS 'C1C)foo' for input: 'C1C)foo' +63: [15:23:06] SMILES Parse Error: extra close parentheses while parsing: C1C)foo +63: [15:23:06] SMILES Parse Error: check for mistakes around position 4: +63: [15:23:06] C1C)foo +63: [15:23:06] ~~~^ +63: [15:23:06] SMILES Parse Error: Failed parsing SMILES 'C1C)foo' for input: 'C1C)foo' 63: =============================================================================== 63: All tests passed (1584 assertions in 68 test cases) 63: @@ -18276,7 +18312,7 @@ 68: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Depictor/Wrap/testDepictor.py" 68: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap 68: Test timeout computed to be: 1500 -61: Randomness seeded to: 3875917205 +61: Randomness seeded to: 4130551587 61: Test 61: 61: ShortAtropisomerNoCoords.cxsmi @@ -18337,16 +18373,16 @@ 61: 61: BMS-986142_atrop5.cxsmi 61: -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: Test 61: 61: BMS-986142_atrop6.cxsmi @@ -18355,25 +18391,25 @@ 61: 61: BMS-986142_atropBad1.cxsmi 61: -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 6 7 61: Test 61: 61: BMS-986142_atropBad2.cxsmi 61: -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 -67: Randomness seeded to: 1075681362 -67: =============================================================================== -67: All tests passed (580 assertions in 18 test cases) -67: - 57/235 Test #67: depictorCatch .......................... Passed 0.16 sec +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 6 7 +65: Randomness seeded to: 4088435139 +65: =============================================================================== +65: All tests passed (14 assertions in 2 test cases) +65: + 57/235 Test #65: v2smiTestCatch ......................... Passed 0.27 sec test 69 Start 69: testMrvToMol @@ -18404,11 +18440,22 @@ 61: 61: JDQ443_atropBad1.cxsmi 61: -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 3 +67: Randomness seeded to: 1482599090 +67: =============================================================================== +67: All tests passed (580 assertions in 18 test cases) +67: + 58/235 Test #67: depictorCatch .......................... Passed 0.30 sec +test 70 + Start 70: fileParsersTest1 + +70: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +70: Test timeout computed to be: 1500 61: Test 61: 61: RP-6306_atrop1.cxsmi @@ -18429,26 +18476,16 @@ 61: 61: RP-6306_atrop5.cxsmi 61: -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: Using new chirality perception -69: Test -69: -69: rxnStereoMarkedCrossed.mrv -69: -69: Test -69: -69: 145323811.mol -69: -69: [05:51:06] unsupported number of radical electrons 5 -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 61: Test 61: 61: RP-6306_atrop6.cxsmi @@ -18457,20 +18494,20 @@ 61: 61: RP-6306_atropBad1.cxsmi 61: -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 4 5 61: Test 61: 61: RP-6306_atropBad2.cxsmi 61: -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 4 5 61: Test 61: 61: RP-6306_3d.cxsmi @@ -18495,24 +18532,87 @@ 61: 61: Sotorasib_atrop5.cxsmi 61: -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored -61: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +61: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 13 ignored +66: [15:23:06] Warning: stereochemistry around double bond may be incorrect in depiction. 61: Test 61: 61: Sotorasib_atropBad1.cxsmi 61: -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -66: [05:51:06] Warning: stereochemistry around double bond may be incorrect in depiction. -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 +61: Test +61: +61: Sotorasib_atropBad2.cxsmi +61: +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +69: Using new chirality perception +69: Test +69: +69: rxnStereoMarkedCrossed.mrv +69: +69: Test +69: +69: 145323811.mol +69: +69: [15:23:06] unsupported number of radical electrons 5 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +61: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 +70: *************************************** +70: *************************************** +70: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +61: Test +61: +61: Sotorasib_3d.cxsmi +61: +61: Test +61: +61: ZM374979_atrop1.cxsmi +61: +61: Test +61: +61: ZM374979_atrop2.cxsmi +61: +61: Test +61: +61: ZM374979_atrop3.cxsmi +61: +61: Test +61: +61: ZM374979_atrop4.cxsmi +61: +61: Test +61: +61: ZM374979_atropBad1.cxsmi +61: +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 + 59/235 Test #66: testDepictor ........................... Passed 0.60 sec +test 71 + Start 71: testAtropisomers + +71: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers +71: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +71: Test timeout computed to be: 1500 +70: [15:23:06] bond with order 0 found on line 7. This is not part of the MDL specification. +71: [15:23:06] ---- Running with POSIX locale ----- 69: Test 69: 69: NewChiralTest.sdf @@ -18545,55 +18645,11 @@ 69: 69: ProblemShort.mol 69: -69: [05:51:06] For a MultipleSgroup expansion, the matching orphaned bond was not found +69: [15:23:06] For a MultipleSgroup expansion, the matching orphaned bond was not found 69: The multiple sgroup will be ignored -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 13 14 -61: Test -61: -61: Sotorasib_atropBad2.cxsmi -61: -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 13 14 -61: Test -61: -61: Sotorasib_3d.cxsmi -61: -61: Test -61: -61: ZM374979_atrop1.cxsmi -61: -61: Test -61: -61: ZM374979_atrop2.cxsmi -61: -61: Test -61: -61: ZM374979_atrop3.cxsmi -61: -61: Test -61: -61: ZM374979_atrop4.cxsmi -61: -61: Test -61: -61: ZM374979_atropBad1.cxsmi -61: -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 58/235 Test #66: testDepictor ........................... Passed 0.40 sec -test 70 - Start 70: fileParsersTest1 - -70: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -70: Test timeout computed to be: 1500 +70: [15:23:06] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +70: [15:23:06] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +70: [15:23:06] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 61: Test 61: 61: Mrtx1719_3d.cxsmi @@ -18618,108 +18674,122 @@ 61: 61: Mrtx1719_atropBad1.cxsmi 61: -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -61: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 -70: *************************************** -70: *************************************** -70: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -36: [05:51:06] Maximum BFS search size exceeded. -36: This is likely due to a highly symmetric fused ring system. -70: [05:51:06] bond with order 0 found on line 7. This is not part of the MDL specification. -36: F/C=C/Cl -36: [H]/C(F)=C(/[H])Cl -36: F/C=C/Cl -36: F/C=C/Cl -36: C/C(F)=C(/C)Cl -70: [05:51:06] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -70: [05:51:06] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -70: [05:51:06] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +61: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 11 12 +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 70: generating smiles 70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 70: converting back -36: [05:51:06] ----------------------- -36: Testing isRingFused 70: check isomorphism - 59/235 Test #36: graphmolMolOpsTest ..................... Passed 1.60 sec -test 71 - Start 71: testAtropisomers +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +71: [15:23:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +71: [15:23:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +68: ..............[15:23:07] SMILES Parse Error: syntax error while parsing: invalidsmiles +68: [15:23:07] SMILES Parse Error: check for mistakes around position 1: +68: [15:23:07] invalidsmiles +68: [15:23:07] ^ +68: [15:23:07] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' +71: [15:23:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: [15:23:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +71: Atropisomers- 1 hits 3 misses +71: Final results: +71: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses + 60/235 Test #71: testAtropisomers ....................... Passed 0.73 sec +test 72 + Start 72: testSquiggleDoubleBonds -71: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testAtropisomers -71: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -71: Test timeout computed to be: 1500 -71: [05:51:06] ---- Running with POSIX locale ----- -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -68: ..............[05:51:06] SMILES Parse Error: syntax error while parsing: invalidsmiles -68: [05:51:06] SMILES Parse Error: check for mistakes around position 1: -68: [05:51:06] invalidsmiles -68: [05:51:06] ^ -68: [05:51:06] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -71: [05:51:06] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds +72: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +72: Randomness seeded to: 881995519 +72: =============================================================================== +72: All tests passed (15 assertions in 3 test cases) +72: + 61/235 Test #72: testSquiggleDoubleBonds ................ Passed 0.04 sec +test 73 + Start 73: testMolSupplier + +73: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +68: ..... +68: ---------------------------------------------------------------------- +68: Ran 19 tests in 0.839s +68: +68: OK +73: [15:23:07] +73: ----------------------------------------- 69: Test 69: 69: badWedgeError.sdf @@ -19032,22 +19102,8 @@ 69: 69: MulticenterSgroup.mrv 69: -69: [05:51:06] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -69: [05:51:06] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -71: [05:51:06] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -68: ..... -68: ---------------------------------------------------------------------- -68: Ran 19 tests in 0.450s -68: -68: OK +69: [15:23:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +69: [15:23:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 69: Test 69: 69: GenericSgroup.mrv @@ -19080,7 +19136,7 @@ 69: 69: MarvinBadMissingMolID.mrv 69: -69: [05:51:06] +69: [15:23:07] 69: 69: **** 69: Test Assert @@ -19091,12 +19147,12 @@ 69: Stacktrace: 69: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 69: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -69: 2# 0x0000AAAAAD98AC5C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 3# 0x0000AAAAAD995D5C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 4# 0x0000AAAAAD984918 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -69: 5# 0x0000FFFFB969229C in /lib/aarch64-linux-gnu/libc.so.6 +69: 2# 0x0000AAAAB028AC5C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 3# 0x0000AAAAB0295D5C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 4# 0x0000AAAAB0284918 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 5# 0x0000FFFFA7C0229C in /lib/aarch64-linux-gnu/libc.so.6 69: 6# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -69: 7# 0x0000AAAAAD984B70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +69: 7# 0x0000AAAAB0284B70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 69: ---------- 69: **** 69: @@ -19226,47 +19282,42 @@ 69: MarvinBadSupMissingAttachOrder.mrv 69: 69: Expected atom, order and bond, for an AttachmentPoint definition in MRV file - 60/235 Test #68: pyDepictor ............................. Passed 0.90 sec -test 72 - Start 72: testSquiggleDoubleBonds - -72: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSquiggleDoubleBonds -72: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 -72: Randomness seeded to: 3040825414 -72: =============================================================================== -72: All tests passed (15 assertions in 3 test cases) -72: - 61/235 Test #72: testSquiggleDoubleBonds ................ Passed 0.05 sec -test 73 - Start 73: testMolSupplier +73: [15:23:07] +73: +73: **** +73: Invariant Violation +73: bad prop value +73: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +73: Failed Expression: nSwaps < 2 +73: ---------- +73: Stacktrace: +73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +73: 2# 0x0000FFFF94575C7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 4# 0x0000AAAAC0E9D59C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 5# 0x0000AAAAC0E92A68 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 6# 0x0000AAAAC0E60E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 7# 0x0000FFFF93B7229C in /lib/aarch64-linux-gnu/libc.so.6 +73: 8# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +73: 9# 0x0000AAAAC0E627F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: ---------- +73: **** +73: + 62/235 Test #68: pyDepictor ............................. Passed 1.50 sec +test 74 + Start 74: testGeneralFileReader -73: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -61: Test -61: -61: AtropCanon1.cxsmi -61: -61: Test -61: -61: AtropCanon2.cxsmi -61: -61: Test -61: -61: AtropCanon3.cxsmi -61: -61: Test -61: -61: BMS-986142_3d_chiral.cxsmi -61: -61: Test -61: -61: BMS-986142_3d.cxsmi -61: -61: =============================================================================== -61: All tests passed (2445 assertions in 29 test cases) -61: +74: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +74: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +74: [15:23:07] +74: ----------------------------------------- +74: [15:23:07] Finished: testDetermineFormat() +74: [15:23:07] ----------------------------------------- +74: +74: [15:23:07] +74: ----------------------------------------- 69: Test 69: 69: marvin03.mrv @@ -19331,15 +19382,16 @@ 69: 69: BMS-986142_atrop5.mrv 69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored - 62/235 Test #61: cxsmilesTest ........................... Passed 1.25 sec -test 74 - Start 74: testGeneralFileReader - -74: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -74: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +73: [15:23:07] Finished: testMolSup() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testRandMolSup() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- 69: Test 69: 69: BMS-986142_atrop6.mrv @@ -19352,34 +19404,47 @@ 69: 69: BMS-986142_atrop8.mrv 69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: 69: BMS-986142_atropBad2.mrv 69: -69: [05:51:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 -71: [05:51:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -71: [05:51:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [05:51:07] -73: ----------------------------------------- -71: Atropisomers- 1 hits 3 misses -71: Final results: -71: Found atropisomers in TestMultInSDF.sdf - 1 hits 4 misses - 63/235 Test #71: testAtropisomers ....................... Passed 0.43 sec -test 75 - Start 75: testMultithreadedMolSupplier - -75: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -75: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 -74: [05:51:07] +69: [15:23:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 +74: [15:23:07] Finished: testSdf() +74: [15:23:07] ----------------------------------------- +74: +74: [15:23:07] 74: ----------------------------------------- -74: [05:51:07] Finished: testDetermineFormat() -74: [05:51:07] ----------------------------------------- +73: [15:23:07] Finished: testSmilesSup() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] ------------------------------------------------------ +73: [15:23:07] SMILES Parse Error: syntax error while parsing: fail +73: [15:23:07] SMILES Parse Error: check for mistakes around position 1: +73: [15:23:07] fail +73: [15:23:07] ^ +73: [15:23:07] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +73: [15:23:07] ERROR: Smiles parse error on line 3 +73: [15:23:07] ERROR: Cannot create molecule from : 'fail' +73: [15:23:07] ------------------------------------------------------ +73: [15:23:07] ------------------------------------------------------ +73: [15:23:07] >>> This may result in an infinite loop. It should finish almost immediately: +73: [15:23:07] <<< done. +73: [15:23:07] Finished: testSmilesSupFromText() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +74: [15:23:07] Finished: testSmi() +74: [15:23:07] ----------------------------------------- 74: -74: [05:51:07] +74: [15:23:07] 74: ----------------------------------------- +73: [15:23:07] Finished: testSmilesWriter() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- 69: Test 69: 69: JDQ443_3d.mrv @@ -19400,31 +19465,104 @@ 69: 69: JDQ443_atropBad1.mrv 69: -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 -73: [05:51:07] +69: [15:23:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 +73: [15:23:07] Finished: testSDWriter() +73: [15:23:07] ----------------------------------------- 73: -73: **** -73: Invariant Violation -73: bad prop value -73: Violation occurred on line 155 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -73: Failed Expression: nSwaps < 2 -73: ---------- -73: Stacktrace: -73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 2# 0x0000FFFF8C2D5C7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 4# 0x0000AAAAAB21D59C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 5# 0x0000AAAAAB212A68 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 6# 0x0000AAAAAB1E0E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 7# 0x0000FFFF8B8D229C in /lib/aarch64-linux-gnu/libc.so.6 -73: 8# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -73: 9# 0x0000AAAAAB1E27F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: ---------- -73: **** +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testSDSupplierEnding() +73: [15:23:07] ----------------------------------------- 73: -75: [05:51:07] -75: ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testSuppliersEmptyFile() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testCisTrans() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testStereoRound() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [15:23:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [15:23:07] Finished: testIssue226() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testTDTSupplier1() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testTDTSupplier2() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testTDTSupplier3() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testSDSupplierFromText() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] ERROR: Problems encountered parsing data fields +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] ERROR: Problems encountered parsing data fields +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] Spurious data before the first property will be ignored +73: [15:23:07] Property will be truncated after the first blank line +73: [15:23:07] Property will be truncated after the first blank line +73: [15:23:07] Property will be truncated after the first blank line +73: [15:23:07] Finished: testSDSupplierStrLax1() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] ERROR: Problems encountered parsing data fields +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] Property will be truncated after the first blank line +73: [15:23:07] Finished: testSDSupplierStrLax2() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] ERROR: Problems encountered parsing data fields +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] ERROR: Problems encountered parsing data fields +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] Spurious data before the first property will be ignored +73: [15:23:07] Property will be truncated after the first blank line +73: [15:23:07] Property will be truncated after the first blank line +73: [15:23:07] Property will be truncated after the first blank line +73: [15:23:07] Finished: testSDSupplierFromTextStrLax1() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] ERROR: Problems encountered parsing data fields +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] Property will be truncated after the first blank line +73: [15:23:07] Finished: testSDSupplierFromTextStrLax2() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testIssue265() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +73: [15:23:07] ERROR: End of data field name not found +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] Explicit valence for atom # 0 F, 2, is greater than permitted +73: [15:23:07] ERROR: Could not sanitize molecule ending on line 16 +73: [15:23:07] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +73: [15:23:07] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] ERROR: Bond line too short: 'M END' on line 18 +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] Finished: testSDErrorHandling() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- 69: Test 69: 69: RP-6306_atrop1.mrv @@ -19445,424 +19583,168 @@ 69: 69: RP-6306_atrop5.mrv 69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: Test -69: -69: RP-6306_atropBad1.mrv -69: -69: [05:51:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 -69: Test -69: -69: RP-6306_atropBad2.mrv -69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 -74: [05:51:07] Finished: testSdf() -74: [05:51:07] ----------------------------------------- +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +73: [15:23:07] Finished: testIssue381() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- +74: [15:23:07] Finished: testMae() +74: [15:23:07] ----------------------------------------- 74: -74: [05:51:07] +74: [15:23:07] 74: ----------------------------------------- -74: [05:51:07] Finished: testSmi() -74: [05:51:07] ----------------------------------------- +74: [15:23:07] Finished: testTdt() +74: [15:23:07] ----------------------------------------- 74: -74: [05:51:07] -74: ----------------------------------------- -69: Test -69: -69: RP-6306_3d.mrv -69: -69: Test -69: -69: Sotorasib_atrop1.mrv -69: -69: Test -69: -69: Sotorasib_atrop2.mrv -69: -69: Test -69: -69: Sotorasib_atrop3.mrv -69: -69: Test -69: -69: Sotorasib_atrop4.mrv -69: -69: Test -69: -69: Sotorasib_atrop5.mrv -69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: Test -69: -69: Sotorasib_atropBad1.mrv -69: -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 -69: Test -69: -69: Sotorasib_atropBad2.mrv -69: -69: [05:51:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 -73: [05:51:07] Finished: testMolSup() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testRandMolSup() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -69: Test -69: -69: Sotorasib_3d.mrv -69: -69: Test -69: -69: ZM374979_atrop1.mrv -69: -69: Test -69: -69: ZM374979_atrop2.mrv -69: -69: Test -69: -69: ZM374979_atrop3.mrv -69: 69: Test 69: -69: ZM374979_atropBad1.mrv +69: RP-6306_atropBad1.mrv 69: -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 -73: [05:51:07] Finished: testSmilesSup() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] ------------------------------------------------------ -73: [05:51:07] SMILES Parse Error: syntax error while parsing: fail -73: [05:51:07] SMILES Parse Error: check for mistakes around position 1: -73: [05:51:07] fail -73: [05:51:07] ^ -73: [05:51:07] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -73: [05:51:07] ERROR: Smiles parse error on line 3 -73: [05:51:07] ERROR: Cannot create molecule from : 'fail' -73: [05:51:07] ------------------------------------------------------ -73: [05:51:07] ------------------------------------------------------ -73: [05:51:07] >>> This may result in an infinite loop. It should finish almost immediately: -73: [05:51:07] <<< done. -73: [05:51:07] Finished: testSmilesSupFromText() -73: [05:51:07] ----------------------------------------- +69: [15:23:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 +73: [15:23:07] Finished: testSetStreamIndices() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testSmilesWriter() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -69: Test -69: -69: mrtx1719_3d.mrv -69: -69: Test -69: -69: mrtx1719_atrop1.mrv -69: -69: Test -69: -69: mrtx1719_atrop2.mrv -69: -69: Test -69: -69: mrtx1719_atrop3.mrv -69: +73: [15:23:07] ----------------------------------------- + 63/235 Test #74: testGeneralFileReader .................. Passed 0.28 sec +test 75 + Start 75: testMultithreadedMolSupplier + +75: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +75: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 69: Test 69: -69: mrtx1719_atropBad1.mrv +69: RP-6306_atropBad2.mrv 69: -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -74: [05:51:07] Finished: testMae() -74: [05:51:07] ----------------------------------------- -74: -74: [05:51:07] -74: ----------------------------------------- -74: [05:51:07] Finished: testTdt() -74: [05:51:07] ----------------------------------------- -74: -73: [05:51:07] Finished: testSDWriter() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- - 64/235 Test #74: testGeneralFileReader .................. Passed 0.23 sec -test 76 - Start 76: testMolWriter - -76: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -76: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -73: [05:51:07] Finished: testSDSupplierEnding() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testSuppliersEmptyFile() -73: [05:51:07] ----------------------------------------- +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [15:23:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +73: [15:23:07] Finished: testMixIterAndRandom() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testCisTrans() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testStereoRound() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [05:51:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [05:51:07] Finished: testIssue226() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testTDTSupplier1() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testTDTSupplier2() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testTDTSupplier3() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testSDSupplierFromText() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] ERROR: Problems encountered parsing data fields -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] ERROR: Problems encountered parsing data fields -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Spurious data before the first property will be ignored -73: [05:51:07] Property will be truncated after the first blank line -73: [05:51:07] Property will be truncated after the first blank line -73: [05:51:07] Property will be truncated after the first blank line -73: [05:51:07] Finished: testSDSupplierStrLax1() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] ERROR: Problems encountered parsing data fields -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Property will be truncated after the first blank line -73: [05:51:07] Finished: testSDSupplierStrLax2() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] ERROR: Problems encountered parsing data fields -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] ERROR: Problems encountered parsing data fields -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Spurious data before the first property will be ignored -73: [05:51:07] Property will be truncated after the first blank line -73: [05:51:07] Property will be truncated after the first blank line -73: [05:51:07] Property will be truncated after the first blank line -73: [05:51:07] Finished: testSDSupplierFromTextStrLax1() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: build: +73: [15:23:07] Finished: testRemoveHs() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] ERROR: Problems encountered parsing data fields -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Property will be truncated after the first blank line -73: [05:51:07] Finished: testSDSupplierFromTextStrLax2() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testGetItemText() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testIssue265() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testForwardSDSupplier() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] ERROR: End of data field name not found -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Explicit valence for atom # 0 F, 2, is greater than permitted -73: [05:51:07] ERROR: Could not sanitize molecule ending on line 16 -73: [05:51:07] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -73: [05:51:07] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] ERROR: Bond line too short: 'M END' on line 18 -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Finished: testSDErrorHandling() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testMissingCRSDSupplier() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testIssue381() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testIssue3482695() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testSetStreamIndices() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] ERROR: Cannot convert 'foo' to unsigned int on line 557 +73: [15:23:07] ERROR: moving to the beginning of the next molecule +75: [15:23:07] +75: ----------------------------------------- +73: [15:23:07] Finished: testIssue3525673() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testMixIterAndRandom() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testBlankLinesInProps() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: build: -73: [05:51:07] Finished: testRemoveHs() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testSkipLines() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testGetItemText() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testGitHub23() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -69: Test -69: -69: FalseAtropisomer.mrv -69: -69: Test -69: -69: AtropEnhancedStereo.mrv -69: -69: Test -69: -69: AtropManyChirals.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced2.mrv -69: +73: [15:23:07] ----------------------------------------- 69: Test 69: -69: AtropManyChiralsEnhanced3.mrv -69: -69: Test -69: -69: AtropManyChiralsEnhanced4.mrv +69: RP-6306_3d.mrv 69: 69: Test 69: -69: BMS-986142_3d_chiral.mrv +69: Sotorasib_atrop1.mrv 69: 69: Test 69: -69: BMS-986142_3d.mrv +69: Sotorasib_atrop2.mrv 69: 69: Test 69: -69: BMS-986142_atrop1.mrv +69: Sotorasib_atrop3.mrv 69: 69: Test 69: -69: BMS-986142_atrop2.mrv +69: Sotorasib_atrop4.mrv 69: 69: Test 69: -69: BMS-986142_atrop3.mrv +69: Sotorasib_atrop5.mrv 69: +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [15:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +73: [15:23:07] Finished: testGitHub88() +73: [15:23:07] ----------------------------------------- +73: +73: [15:23:07] ----------------------------------------- 69: Test 69: -69: BMS-986142_atrop4.mrv +69: Sotorasib_atropBad1.mrv 69: +69: [15:23:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: Test 69: -69: BMS-986142_atrop5.mrv +69: Sotorasib_atropBad2.mrv 69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -73: [05:51:07] Finished: testForwardSDSupplier() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testMissingCRSDSupplier() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testIssue3482695() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] ERROR: Cannot convert 'foo' to unsigned int on line 557 -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Finished: testIssue3525673() -73: [05:51:07] ----------------------------------------- +69: [15:23:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 +73: [15:23:07] Finished: testGitHub2285() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testBlankLinesInProps() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +73: [15:23:07] ERROR: Smiles parse error on line 1 +73: [15:23:07] ERROR: Cannot create molecule from : 'c1ccccc' +73: [15:23:07] SMILES Parse Error: extra open parentheses while parsing: C(C +73: [15:23:07] SMILES Parse Error: check for mistakes around position 2: +73: [15:23:07] C(C +73: [15:23:07] ~^ +73: [15:23:07] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +73: [15:23:07] ERROR: Smiles parse error on line 3 +73: [15:23:07] ERROR: Cannot create molecule from : 'C(C' +73: [15:23:07] Explicit valence for atom # 1 C, 5, is greater than permitted +73: [15:23:07] ERROR: Could not sanitize molecule on line 5 +73: [15:23:07] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +73: [15:23:07] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [15:23:07] ERROR: Could not sanitize molecule ending on line 21 +73: [15:23:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [15:23:07] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [15:23:07] ERROR: Could not sanitize molecule ending on line 21 +73: [15:23:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [15:23:07] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [15:23:07] ERROR: Could not sanitize molecule ending on line 21 +73: [15:23:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [15:23:07] ERROR: Atom line too short: ' -9.6' on line 28 +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] Explicit valence for atom # 1 F, 2, is greater than permitted +73: [15:23:07] ERROR: Could not sanitize molecule ending on line 21 +73: [15:23:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +73: [15:23:07] ERROR: Atom line too short: ' -9.6' on line 28 +73: [15:23:07] ERROR: moving to the beginning of the next molecule +73: [15:23:07] Finished: testGitHub2479() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testSkipLines() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testGitHub23() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testGitHub88() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testGitHub2285() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -73: [05:51:07] ERROR: Smiles parse error on line 1 -73: [05:51:07] ERROR: Cannot create molecule from : 'c1ccccc' -73: [05:51:07] SMILES Parse Error: extra open parentheses while parsing: C(C -73: [05:51:07] SMILES Parse Error: check for mistakes around position 2: -73: [05:51:07] C(C -73: [05:51:07] ~^ -73: [05:51:07] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -73: [05:51:07] ERROR: Smiles parse error on line 3 -73: [05:51:07] ERROR: Cannot create molecule from : 'C(C' -73: [05:51:07] Explicit valence for atom # 1 C, 5, is greater than permitted -73: [05:51:07] ERROR: Could not sanitize molecule on line 5 -73: [05:51:07] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -73: [05:51:07] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [05:51:07] ERROR: Could not sanitize molecule ending on line 21 -73: [05:51:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [05:51:07] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [05:51:07] ERROR: Could not sanitize molecule ending on line 21 -73: [05:51:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [05:51:07] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [05:51:07] ERROR: Could not sanitize molecule ending on line 21 -73: [05:51:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [05:51:07] ERROR: Atom line too short: ' -9.6' on line 28 -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Explicit valence for atom # 1 F, 2, is greater than permitted -73: [05:51:07] ERROR: Could not sanitize molecule ending on line 21 -73: [05:51:07] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -73: [05:51:07] ERROR: Atom line too short: ' -9.6' on line 28 -73: [05:51:07] ERROR: moving to the beginning of the next molecule -73: [05:51:07] Finished: testGitHub2479() -73: [05:51:07] ----------------------------------------- -73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] +73: [15:23:07] ----------------------------------------- +73: [15:23:07] 73: 73: **** -69: Test -69: -69: BMS-986142_atrop6.mrv -69: -69: Test -69: -69: BMS-986142_atrop7.mrv -69: -69: Test -69: -69: BMS-986142_atrop8.mrv -69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: Test -69: -69: BMS-986142_atropBad2.mrv -69: -69: [05:51:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 73: Invariant Violation 73: bad chiral bond 73: Violation occurred on line 161 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp @@ -19871,24 +19753,54 @@ 73: Stacktrace: 73: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 73: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -73: 2# 0x0000FFFF8C2D61A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +73: 2# 0x0000FFFF945761A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 73: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -73: 4# 0x0000AAAAAB1E36A0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 5# 0x0000AAAAAB1E2514 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -73: 6# 0x0000FFFF8B8D229C in /lib/aarch64-linux-gnu/libc.so.6 +73: 4# 0x0000AAAAC0E636A0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 5# 0x0000AAAAC0E62514 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 6# 0x0000FFFF93B7229C in /lib/aarch64-linux-gnu/libc.so.6 73: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -73: 8# 0x0000AAAAAB1E27F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +73: 8# 0x0000AAAAC0E627F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 73: ---------- 73: **** 73: -73: [05:51:07] Finished: testGitHub2881() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] Finished: testGitHub2881() +73: [15:23:07] ----------------------------------------- 73: -73: [05:51:07] ----------------------------------------- -73: [05:51:07] Finished: testGitHub3517() -73: [05:51:07] ----------------------------------------- +73: [15:23:07] ----------------------------------------- +73: [15:23:07] Finished: testGitHub3517() +73: [15:23:07] ----------------------------------------- 73: - 65/235 Test #73: testMolSupplier ........................ Passed 0.34 sec + 64/235 Test #73: testMolSupplier ........................ Passed 0.62 sec +test 76 + Start 76: testMolWriter + +76: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +76: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +61: Test +61: +61: AtropCanon1.cxsmi +61: +61: Test +61: +61: AtropCanon2.cxsmi +61: +61: Test +61: +61: AtropCanon3.cxsmi +61: +61: Test +61: +61: BMS-986142_3d_chiral.cxsmi +61: +61: Test +61: +61: BMS-986142_3d.cxsmi +61: +61: =============================================================================== +61: All tests passed (2445 assertions in 29 test cases) +61: + 65/235 Test #61: cxsmilesTest ........................... Passed 2.21 sec test 77 Start 77: testTplParser @@ -19897,26 +19809,59 @@ 77: Test timeout computed to be: 1500 69: Test 69: -69: JDQ443_3d.mrv +69: Sotorasib_3d.mrv 69: 69: Test 69: -69: JDQ443_atrop1.mrv +69: ZM374979_atrop1.mrv 69: 69: Test 69: -69: JDQ443_atrop2.mrv +69: ZM374979_atrop2.mrv 69: 69: Test 69: -69: JDQ443_atrop3.mrv +69: ZM374979_atrop3.mrv 69: 69: Test 69: -69: JDQ443_atropBad1.mrv +69: ZM374979_atropBad1.mrv 69: -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 - 66/235 Test #77: testTplParser .......................... Passed 0.04 sec +69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +70: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [15:23:08] deprecated group abbreviation ignored on line 24 +70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +70: [15:23:08] +70: +70: **** +70: Post-condition Violation +70: Element 'Mv' not found +70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +70: Failed Expression: anum > -1 +70: ---------- +70: Stacktrace: +70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 3# 0x0000FFFFB8CA7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 4# 0x0000FFFFB8CB5BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 5# 0x0000FFFFB8CB6AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 9# 0x0000AAAAC525F83C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 10# 0x0000AAAAC52D4B44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 11# 0x0000AAAAC5245CB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 12# 0x0000FFFFB837229C in /lib/aarch64-linux-gnu/libc.so.6 +70: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +70: 14# 0x0000AAAAC5245EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: ---------- +70: **** +70: + 66/235 Test #77: testTplParser .......................... Passed 0.05 sec test 78 Start 78: testMol2ToMol @@ -19925,147 +19870,106 @@ 78: Test timeout computed to be: 1500 69: Test 69: -69: RP-6306_atrop1.mrv -69: -69: Test -69: -69: RP-6306_atrop2.mrv -69: -69: Test -69: -69: RP-6306_atrop3.mrv -69: -69: Test -69: -69: RP-6306_atrop4.mrv +69: mrtx1719_3d.mrv 69: 69: Test 69: -69: RP-6306_atrop5.mrv +69: mrtx1719_atrop1.mrv 69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: Test 69: -69: RP-6306_atropBad1.mrv +69: mrtx1719_atrop2.mrv 69: -69: [05:51:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: Test 69: -69: RP-6306_atropBad2.mrv +69: mrtx1719_atrop3.mrv 69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 69: Test 69: -69: RP-6306_3d.mrv +69: mrtx1719_atropBad1.mrv 69: +69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 + 67/235 Test #78: testMol2ToMol .......................... Passed 0.08 sec +test 79 + Start 79: testSequence + +79: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence +79: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +79: Test timeout computed to be: 1500 69: Test 69: -69: Sotorasib_atrop1.mrv +69: FalseAtropisomer.mrv 69: 69: Test 69: -69: Sotorasib_atrop2.mrv +69: AtropEnhancedStereo.mrv 69: 69: Test 69: -69: Sotorasib_atrop3.mrv +69: AtropManyChirals.mrv 69: 69: Test 69: -69: Sotorasib_atrop4.mrv +69: AtropManyChiralsEnhanced.mrv 69: 69: Test 69: -69: Sotorasib_atrop5.mrv +69: AtropManyChiralsEnhanced2.mrv 69: -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -69: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 69: Test 69: -69: Sotorasib_atropBad1.mrv +69: AtropManyChiralsEnhanced3.mrv 69: -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 69: Test 69: -69: Sotorasib_atropBad2.mrv +69: AtropManyChiralsEnhanced4.mrv 69: -69: [05:51:07] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 69: Test 69: -69: Sotorasib_3d.mrv +69: BMS-986142_3d_chiral.mrv 69: 69: Test 69: -69: ZM374979_atrop1.mrv +69: BMS-986142_3d.mrv 69: 69: Test 69: -69: ZM374979_atrop2.mrv +69: BMS-986142_atrop1.mrv 69: 69: Test 69: -69: ZM374979_atrop3.mrv +69: BMS-986142_atrop2.mrv 69: 69: Test 69: -69: ZM374979_atropBad1.mrv +69: BMS-986142_atrop3.mrv 69: -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 - 67/235 Test #78: testMol2ToMol .......................... Passed 0.10 sec -test 79 - Start 79: testSequence - -79: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence -79: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -79: Test timeout computed to be: 1500 69: Test 69: -69: mrtx1719_3d.mrv +69: BMS-986142_atrop4.mrv 69: 69: Test 69: -69: mrtx1719_atrop1.mrv +69: BMS-986142_atrop5.mrv 69: +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +70: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +70: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 69: Test 69: -69: mrtx1719_atrop2.mrv +69: BMS-986142_atrop6.mrv 69: 69: Test 69: -69: mrtx1719_atrop3.mrv +69: BMS-986142_atrop7.mrv 69: 69: Test 69: -69: mrtx1719_atropBad1.mrv +69: BMS-986142_atrop8.mrv 69: -69: [05:51:07] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 -76: [05:51:07] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -76: 0.40201265 0.40201265 -76: -0.13299436 -0.13299436 -76: 1.00000017 1.00000017 -76: 0.8762226 0.8762226 -76: 0.9973909 0.9973909 -76: 1.00000003 1.00000003 -76: 0.36613799 0.36613799 -76: 2.1107185 2.1107185 -76: 0.99999982 0.99999982 -76: 2.48696157 2.48696157 -76: 1.00479935 1.00479935 -76: 0.99999999 0.99999999 -76: 3.03311841 3.03311841 -76: 2.23739955 2.23739955 -76: 1.0000001 1.0000001 -76: 3.00772337 3.00772337 -76: 0.37399294 0.37399294 -76: 2.07713325 2.07713325 -76: 3.0077234 3.0077234 -76: 0.37399312 0.37399312 -76: -0.07713336 -0.07713336 -76: [05:51:07] bond with order 0 found on line 11. This is not part of the MDL specification. -76: [05:51:07] bond with order 0 found on line 16. This is not part of the MDL specification. +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 79: Sequence: GREG 79: HELM: PEPTIDE1{G.R.E.G}$$$$ 79: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -21050,14 +20954,19 @@ 79: CONECT 27 28 28 29 79: END 79: - 68/235 Test #76: testMolWriter .......................... Passed 0.31 sec - 69/235 Test #79: testSequence ........................... Passed 0.07 sec + 68/235 Test #79: testSequence ........................... Passed 0.06 sec test 80 Start 80: testExtendedStereoParsing 80: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 80: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 80: Test timeout computed to be: 1500 +69: Test +69: +69: BMS-986142_atropBad2.mrv +69: +69: [15:23:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 29 + 69/235 Test #80: testExtendedStereoParsing .............. Passed 0.02 sec test 81 Start 81: fileParsersCatchTest @@ -21066,167 +20975,79 @@ 81: Test timeout computed to be: 1500 69: Test 69: -69: AlexRxn.mrv -69: -69: Test -69: -69: BadReactionSign.mrv -69: -69: Test -69: -69: bondArray_node.mrv -69: -69: Test -69: -69: marvin03.mrv -69: -69: Test -69: -69: marvin04.mrv -69: -69: Test -69: -69: marvin08.mrv -69: -69: Test -69: -69: marvin09.mrv -69: -69: Test -69: -69: marvin11.mrv -69: -69: Test -69: -69: marvin05.mrv -69: -69: Test -69: -69: EmptyRxn.mrv -69: -69: [05:51:07] initialization failed -69: Test -69: -69: RxnNoCoords.mrv -69: -69: Test -69: -69: mrvValenceZero.mrv -69: -69: Test -69: -69: condition_coordinates_mpoint.mrv -69: -69: Test -69: -69: marvin01.mrv -69: -69: Test -69: -69: aspirineSynthesisWithAttributes.mrv -69: -69: Test -69: -69: marvin01.mrv -69: -69: Test -69: -69: NewChiralTest -69: -69: Test -69: -69: NewChiralTest -69: -69: Test -69: -69: NewChiralTestNoChiral -69: -69: Test -69: -69: NewChiralTestNoChiral -69: -69: Test -69: -69: NewChiralTest2 +69: JDQ443_3d.mrv 69: 69: Test 69: -69: NewChiralTest2 +69: JDQ443_atrop1.mrv 69: 69: Test 69: -69: NewChiralTest2AllChiral +69: JDQ443_atrop2.mrv 69: 69: Test 69: -69: NewChiralTest2AllChiral +69: JDQ443_atrop3.mrv 69: 69: Test 69: -69: Vendor839 +69: JDQ443_atropBad1.mrv 69: +69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 17 21 69: Test 69: -69: DoubleBondChain +69: RP-6306_atrop1.mrv 69: 69: Test 69: -69: Na_Mg_Al_OH +69: RP-6306_atrop2.mrv 69: 69: Test 69: -69: Pb +69: RP-6306_atrop3.mrv 69: 69: Test 69: -69: O_Mg_Si +69: RP-6306_atrop4.mrv 69: 69: Test 69: -69: SquiggleBond +69: RP-6306_atrop5.mrv 69: +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored 69: Test 69: -69: BigMacrocycle +69: RP-6306_atropBad1.mrv 69: +69: [15:23:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 2 8 69: Test 69: -69: Smiles1 +69: RP-6306_atropBad2.mrv 69: - 70/235 Test #69: testMrvToMol ........................... Passed 1.45 sec - 71/235 Test #80: testExtendedStereoParsing .............. Passed 0.04 sec -test 82 - Start 82: testPropertyLists - -82: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -82: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -82: Test timeout computed to be: 1500 -test 83 - Start 83: XYZFileParserCatchTest - -83: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -83: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -83: Test timeout computed to be: 1500 -81: Randomness seeded to: 3535802313 -81: [05:51:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -81: [05:51:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -81: [05:51:07] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [05:51:07] SGroup 1 is invalid and will be ignored -81: [05:51:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -81: [05:51:07] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [05:51:07] SGroup 1 is invalid and will be ignored -81: [05:51:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -81: [05:51:07] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -81: [05:51:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -81: [05:51:07] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -81: [05:51:07] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [05:51:07] SGroup 1 is invalid and will be ignored -81: [05:51:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -81: [05:51:07] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -81: [05:51:07] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -81: [05:51:07] SGroup 1 is invalid and will be ignored -81: [05:51:07] SGroup 3 referenced on line 40 not found. -81: [05:51:07] +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 2 ignored +69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 2 8 +81: Randomness seeded to: 3915011631 +81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +81: [15:23:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [15:23:08] SGroup 1 is invalid and will be ignored +81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +81: [15:23:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [15:23:08] SGroup 1 is invalid and will be ignored +81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +81: [15:23:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +81: [15:23:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +81: [15:23:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [15:23:08] SGroup 1 is invalid and will be ignored +81: [15:23:08] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +81: [15:23:08] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +81: [15:23:08] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +81: [15:23:08] SGroup 1 is invalid and will be ignored +81: [15:23:08] SGroup 3 referenced on line 40 not found. +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21239,24 +21060,24 @@ 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB29FEE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFFBA89EE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# 0x0000AAAABAA19D7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 7# 0x0000AAAABD589D7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 16# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] SGroup 3 referenced on line 40 not found. -81: [05:51:07] +81: [15:23:08] SGroup 3 referenced on line 40 not found. +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21269,29 +21090,29 @@ 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB29FEE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFFBA89EE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 7# 0x0000AAAABAA19DFC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 7# 0x0000AAAABD589DFC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 16# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] no bonds -81: [05:51:07] SGroup 1 is invalid and will be ignored -81: [05:51:07] SGroup line too short: 'M SBV 1 6' on line 42 -81: [05:51:07] SGroup 1 is invalid and will be ignored -81: [05:51:07] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -81: [05:51:07] SGroup 2 is invalid and will be ignored -81: [05:51:07] +81: [15:23:08] no bonds +81: [15:23:08] SGroup 1 is invalid and will be ignored +81: [15:23:08] SGroup line too short: 'M SBV 1 6' on line 42 +81: [15:23:08] SGroup 1 is invalid and will be ignored +81: [15:23:08] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +81: [15:23:08] SGroup 2 is invalid and will be ignored +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21305,23 +21126,23 @@ 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29FEDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA89EDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAABAA1A7A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAABD58A7A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21335,24 +21156,24 @@ 81: 2# RDKit::ROMol::getUniqueBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addBondWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29FEDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA89EDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAABAA1A824 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAABD58A824 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] bookmark not found -81: [05:51:07] +81: [15:23:08] bookmark not found +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21366,25 +21187,25 @@ 81: 2# RDKit::SubstanceGroup::getBondType(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addCState(unsigned int, RDGeom::Point3D const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000SBVLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29FEE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA89EE88 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAABAA1A824 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAABD58A824 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] bond is not part of the SubstanceGroup -81: [05:51:07] SGroup 2 is invalid and will be ignored -81: [05:51:07] +81: [15:23:08] bond is not part of the SubstanceGroup +81: [15:23:08] SGroup 2 is invalid and will be ignored +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21398,23 +21219,23 @@ 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29FEDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA89EDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAABAA1AB14 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAABD58AB14 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21428,29 +21249,65 @@ 81: 2# RDKit::ROMol::getUniqueAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 3# RDKit::SubstanceGroup::addAtomWithBookmark(int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 81: 4# RDKit::SGroupParsing::ParseSGroupV2000VectorDataLine(std::map, std::allocator > >&, RDKit::RWMol*, std::__cxx11::basic_string, std::allocator > const&, unsigned int, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29FEDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA89EDF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 8# 0x0000AAAABAA1AB94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 8# 0x0000AAAABD58AB94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 17# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 17# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] bookmark not found -81: [05:51:07] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -81: [05:51:07] SGroup 2 is invalid and will be ignored -81: [05:51:07] WARNING: final character of V3000 array is not ')' -81: [05:51:07] +81: [15:23:08] bookmark not found +81: [15:23:08] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +81: [15:23:08] SGroup 2 is invalid and will be ignored +81: [15:23:08] WARNING: final character of V3000 array is not ')' +81: [15:23:08] 81: 81: **** +69: Test +69: +69: RP-6306_3d.mrv +69: +69: Test +69: +69: Sotorasib_atrop1.mrv +69: +69: Test +69: +69: Sotorasib_atrop2.mrv +69: +69: Test +69: +69: Sotorasib_atrop3.mrv +69: +69: Test +69: +69: Sotorasib_atrop4.mrv +69: +69: Test +69: +69: Sotorasib_atrop5.mrv +69: +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: [15:23:08] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +69: Test +69: +69: Sotorasib_atropBad1.mrv +69: +69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 7 20 +69: Test +69: +69: Sotorasib_atropBad2.mrv +69: +69: [15:23:08] The bonds on one end of an atropisomer are both UP or both DOWN - atoms are: 7 20 81: Pre-condition Violation 81: bookmark not found 81: Violation occurred on line 267 in file ./Code/GraphMol/ROMol.cpp @@ -21466,21 +21323,21 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABAA18798 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD588798 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] WARNING: final character of V3000 array is not ')' -81: [05:51:07] +81: [15:23:08] WARNING: final character of V3000 array is not ')' +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21498,23 +21355,23 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABAA18814 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD588814 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] bookmark not found -81: [05:51:07] SGroup 1 is invalid and will be ignored -81: [05:51:07] WARNING: final character of V3000 array is not ')' -81: [05:51:07] +81: [15:23:08] bookmark not found +81: [15:23:08] SGroup 1 is invalid and will be ignored +81: [15:23:08] WARNING: final character of V3000 array is not ')' +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21532,21 +21389,21 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABAA18AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD588AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] WARNING: final character of V3000 array is not ')' -81: [05:51:07] +81: [15:23:08] WARNING: final character of V3000 array is not ')' +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21564,22 +21421,22 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABAA18B64 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD588B64 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] bookmark not found -81: [05:51:07] SGroup 1 is invalid and will be ignored -81: [05:51:07] +81: [15:23:08] bookmark not found +81: [15:23:08] SGroup 1 is invalid and will be ignored +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21597,20 +21454,20 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABAA18E38 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD588E38 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21628,22 +21485,22 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABAA18EB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD588EB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] bookmark not found -81: [05:51:07] SGroup 2 is invalid and will be ignored -81: [05:51:07] +81: [15:23:08] bookmark not found +81: [15:23:08] SGroup 2 is invalid and will be ignored +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21661,20 +21518,20 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABAA19188 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD589188 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21692,41 +21549,51 @@ 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABAA19204 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD589204 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] bookmark not found -81: [05:51:07] SGroup 2 is invalid and will be ignored -81: [05:51:07] Explicit valence for atom # 2 O, 3, is greater than permitted -81: [05:51:07] Explicit valence for atom # 1 O, 3, is greater than permitted -81: [05:51:07] Explicit valence for atom # 1 C, 5, is greater than permitted -82: Randomness seeded to: 1244767474 -82: =============================================================================== -82: All tests passed (95 assertions in 4 test cases) -82: -81: [05:51:07] sanitize [05:51:07] UNK: [05:51:07] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. - 72/235 Test #82: testPropertyLists ...................... Passed 0.07 sec -test 84 - Start 84: cdxmlParserCatchTest - -84: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -84: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -84: Test timeout computed to be: 1500 -81: [05:51:07] skipping block at line 7: 'BEGIN ATOM' +81: [15:23:08] bookmark not found +81: [15:23:08] SGroup 2 is invalid and will be ignored +81: [15:23:08] Explicit valence for atom # 2 O, 3, is greater than permitted +81: [15:23:08] Explicit valence for atom # 1 O, 3, is greater than permitted +81: [15:23:08] Explicit valence for atom # 1 C, 5, is greater than permitted +69: Test +69: +69: Sotorasib_3d.mrv +69: +69: Test +69: +69: ZM374979_atrop1.mrv +69: +69: Test +69: +69: ZM374979_atrop2.mrv +69: +69: Test +69: +69: ZM374979_atrop3.mrv +69: +69: Test +69: +69: ZM374979_atropBad1.mrv +69: +69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 0 31 +81: [15:23:08] sanitize [15:23:08] UNK: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +81: [15:23:08] skipping block at line 7: 'BEGIN ATOM' 81: ATOM 1 CHLO CHL 0 0.000 0.000 0.000 1.00 0.00 CL 81: END 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21738,21 +21605,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::SDMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAABAA4EEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAABAA0B1A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAABD57B1A4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21764,21 +21631,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::ForwardSDMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAABAA4EEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAABAA0B314 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAABD57B314 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21790,21 +21657,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::SmilesMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAABAA4EEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAABAA0B648 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAABD57B648 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21816,21 +21683,21 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::TDTMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAABAA4EEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAABAA0B8E4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAABD57B8E4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -21842,29 +21709,74 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000AAAABAA4EEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 4# 0x0000AAAABAA0BADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 3# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 4# 0x0000AAAABD57BADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] Found a SCD/SED line with missing/empty SDT specification at line 21 -81: [05:51:07] Found a SCD/SED line with missing/empty SDT specification at line 20 -81: [05:51:07] BEGIN SGROUP line not found on line 14 -81: [05:51:07] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -81: [05:51:07] END SGROUP line not found on line 14 -81: [05:51:07] END SGROUP line not found on line 14 -81: [05:51:07] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -81: [05:51:07] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -81: [05:51:07] +81: [15:23:08] Found a SCD/SED line with missing/empty SDT specification at line 21 +81: [15:23:08] Found a SCD/SED line with missing/empty SDT specification at line 20 +81: [15:23:08] BEGIN SGROUP line not found on line 14 +69: Test +69: +69: mrtx1719_3d.mrv +69: +69: Test +69: +69: mrtx1719_atrop1.mrv +69: +69: Test +69: +69: mrtx1719_atrop2.mrv +69: +69: Test +69: +69: mrtx1719_atrop3.mrv +69: +69: Test +69: +69: mrtx1719_atropBad1.mrv +69: +69: [15:23:08] The 2 defining bonds for an atropisomer are co-planar - atoms are: 15 16 +70: ---------------------------------- +70: ---------------------------------- +70: [15:23:08] +70: +70: **** +70: Pre-condition Violation +70: rlabel out of range for MDL files +70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp +70: Failed Expression: rlabel >= 0 && rlabel < 100 +70: ---------- +70: Stacktrace: +70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +70: 3# 0x0000AAAAC526F2FC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 4# 0x0000AAAAC52D4BA4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 5# 0x0000AAAAC5245CB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 6# 0x0000FFFFB837229C in /lib/aarch64-linux-gnu/libc.so.6 +70: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +70: 8# 0x0000AAAAC5245EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: ---------- +70: **** +70: +70: [15:23:08] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +81: [15:23:08] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +81: [15:23:08] END SGROUP line not found on line 14 +81: [15:23:08] END SGROUP line not found on line 14 +81: [15:23:08] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +81: [15:23:08] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +81: [15:23:08] 81: 81: **** 81: Range Error @@ -21879,49 +21791,38 @@ 81: 3# RDKit::FileParserUtils::finishMolProcessing(RDKit::RWMol*, bool, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 4# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 5# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 6# 0x0000AAAABAA4EB34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAABAA10B30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 6# 0x0000AAAABD5BEB34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAABD580B30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 15# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 16# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -81: [05:51:07] Multiple ATTCHPT values for atom 2 on line 9 -81: [05:51:07] Found a SCD/SED line with missing/empty SDT specification at line 12 -81: [05:51:07] SMARTS Parse Error: syntax error while parsing: [#6;R -81: [05:51:07] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -81: [05:51:07] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -81: [05:51:07] Skipping empty SMARTS value for SMARTSQ. -81: [05:51:07] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -81: [05:51:07] Found a SCD/SED line with missing/empty SDT specification at line 12 -83: Randomness seeded to: 1582854103 -83: =============================================================================== -83: All tests passed (100 assertions in 2 test cases) -83: - 73/235 Test #83: XYZFileParserCatchTest ................. Passed 0.07 sec -test 85 - Start 85: molfileStereoCatchTest - -85: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -85: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -85: Test timeout computed to be: 1500 -81: [05:51:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -81: [05:51:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -81: [05:51:07] WARNING: Skipping property bar because the value includes an illegal blank line -81: [05:51:07] WARNING: Skipping property baz because the value includes an illegal blank line -81: [05:51:07] WARNING: Skipping property bletch +81: [15:23:08] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +81: [15:23:08] Multiple ATTCHPT values for atom 2 on line 9 +81: [15:23:08] Found a SCD/SED line with missing/empty SDT specification at line 12 +81: [15:23:08] SMARTS Parse Error: syntax error while parsing: [#6;R +81: [15:23:08] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +81: [15:23:08] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +81: [15:23:08] Skipping empty SMARTS value for SMARTSQ. +81: [15:23:08] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +81: [15:23:08] Found a SCD/SED line with missing/empty SDT specification at line 12 +81: [15:23:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +81: [15:23:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +81: [15:23:08] WARNING: Skipping property bar because the value includes an illegal blank line +81: [15:23:08] WARNING: Skipping property baz because the value includes an illegal blank line +81: [15:23:08] WARNING: Skipping property bletch 81: nope because the name includes a newline -81: [05:51:07] WARNING: Skipping property bletch +81: [15:23:08] WARNING: Skipping property bletch 81: nope2 because the name includes a newline -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Post-condition Violation @@ -21933,26 +21834,26 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000FFFFB29E7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB29F8230 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29F8E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x0000FFFFBA887FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFFBA898230 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA898E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABA9E4FB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD554FB4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Post-condition Violation @@ -21964,26 +21865,26 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000FFFFB29E7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB29F8230 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29F8E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x0000FFFFBA887FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFFBA898230 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA898E6C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV3000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABA9E48D8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD5548D8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Post-condition Violation @@ -21995,26 +21896,26 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000FFFFB29E7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB29F5BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29F6AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x0000FFFFBA887FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFFBA895BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA896AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABA9E4F70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD554F70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Post-condition Violation @@ -22026,27 +21927,27 @@ 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 3# 0x0000FFFFB29E7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000FFFFB29F5BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 5# 0x0000FFFFB29F6AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 3# 0x0000FFFFBA887FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 4# 0x0000FFFFBA895BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 5# 0x0000FFFFBA896AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 8# RDKit::v2::FileParsers::MolFromMolBlock(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 9# 0x0000AAAABA9E4CA8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 13# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 14# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 15# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 16# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 9# 0x0000AAAABD554CA8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 15# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 16# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 17# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 18# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 18# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] atom 3 has a negative isotope value. line: 15 -81: [05:51:07] +81: [15:23:08] atom 3 has a negative isotope value. line: 15 +81: [15:23:08] 81: 81: **** 81: Invariant Violation @@ -22057,23 +21958,23 @@ 81: Stacktrace: 81: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -81: 2# 0x0000FFFFB2AB5C7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +81: 2# 0x0000FFFFBA955C7C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# RDKit::v2::FileParsers::MaeMolSupplier::next() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000AAAABAA4EEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAABAA21EA0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 12# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 4# 0x0000AAAABD5BEEC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAABD591EA0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 12# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 14# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 14# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -81: [05:51:07] +81: [15:23:08] 81: 81: **** 81: Pre-condition Violation @@ -22086,164 +21987,303 @@ 81: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 81: 2# RDKit::v2::FileParsers::MaeMolSupplier::init() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 81: 3# RDKit::v2::FileParsers::MaeMolSupplier::reset() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -81: 4# 0x0000AAAABAA221C4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 5# 0x0000AAAABAA90B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 6# 0x0000AAAABAA91540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 7# 0x0000AAAABAA91974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 8# 0x0000AAAABAA64E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 9# 0x0000AAAABAA65364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 10# 0x0000AAAABA9DC1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -81: 11# 0x0000FFFFB20C229C in /lib/aarch64-linux-gnu/libc.so.6 +81: 4# 0x0000AAAABD5921C4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 5# 0x0000AAAABD600B8C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 6# 0x0000AAAABD601540 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 7# 0x0000AAAABD601974 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 8# 0x0000AAAABD5D4E18 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 9# 0x0000AAAABD5D5364 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 10# 0x0000AAAABD54C1F0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 11# 0x0000FFFFB9F6229C in /lib/aarch64-linux-gnu/libc.so.6 81: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -81: 13# 0x0000AAAABA9DC2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +81: 13# 0x0000AAAABD54C2B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 81: ---------- 81: **** 81: -70: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [05:51:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [05:51:07] deprecated group abbreviation ignored on line 24 -70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -70: [05:51:07] -70: -70: **** -70: Post-condition Violation -70: Element 'Mv' not found -70: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -70: Failed Expression: anum > -1 -70: ---------- -70: Stacktrace: -70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 3# 0x0000FFFF988F7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 4# 0x0000FFFF98905BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 5# 0x0000FFFF98906AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 9# 0x0000AAAABF49F83C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 10# 0x0000AAAABF514B44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 11# 0x0000AAAABF485CB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 12# 0x0000FFFF97FC229C in /lib/aarch64-linux-gnu/libc.so.6 -70: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -70: 14# 0x0000AAAABF485EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: ---------- -70: **** -70: -85: Randomness seeded to: 1095464887 -85: [05:51:07] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [05:51:07] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [05:51:07] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -85: [05:51:07] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +76: 0.40201265 0.40201265 +76: -0.13299436 -0.13299436 +76: 1.00000017 1.00000017 +76: 0.8762226 0.8762226 +76: 0.9973909 0.9973909 +76: 1.00000003 1.00000003 +76: 0.36613799 0.36613799 +76: 2.1107185 2.1107185 +76: 0.99999982 0.99999982 +76: 2.48696157 2.48696157 +76: 1.00479935 1.00479935 +76: 0.99999999 0.99999999 +76: 3.03311841 3.03311841 +76: 2.23739955 2.23739955 +76: 1.0000001 1.0000001 +76: 3.00772337 3.00772337 +76: 0.37399294 0.37399294 +76: 2.07713325 2.07713325 +76: 3.0077234 3.0077234 +76: 0.37399312 0.37399312 +76: -0.07713336 -0.07713336 +69: Test +69: +69: AlexRxn.mrv +69: +69: Test +69: +69: BadReactionSign.mrv +69: +69: Test +69: +69: bondArray_node.mrv +69: +69: Test +69: +69: marvin03.mrv +69: +69: Test +69: +69: marvin04.mrv +69: +69: Test +69: +69: marvin08.mrv +69: +69: Test +69: +69: marvin09.mrv +69: +69: Test +69: +69: marvin11.mrv +69: +69: Test +69: +69: marvin05.mrv +69: +69: Test +69: +69: EmptyRxn.mrv +69: +69: [15:23:08] initialization failed +76: [15:23:08] bond with order 0 found on line 11. This is not part of the MDL specification. +76: [15:23:08] bond with order 0 found on line 16. This is not part of the MDL specification. + 70/235 Test #76: testMolWriter .......................... Passed 0.56 sec +test 82 + Start 82: testPropertyLists + +82: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +82: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +82: Test timeout computed to be: 1500 +81: [15:23:08] ERROR: molecules without atoms cannot be exported to Maestro files. +81: [15:23:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +81: [15:23:08] ERROR: the mol cannot be kekulized, and will not be written to the output file. +81: [15:23:08] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +69: Test +69: +69: RxnNoCoords.mrv +69: +69: Test +69: +69: mrvValenceZero.mrv +69: +69: Test +69: +69: condition_coordinates_mpoint.mrv +69: +69: Test +69: +69: marvin01.mrv +69: +69: Test +69: +69: aspirineSynthesisWithAttributes.mrv +69: +69: Test +69: +69: marvin01.mrv +69: +69: Test +69: +69: NewChiralTest +69: +69: Test +69: +69: NewChiralTest +69: +69: Test +69: +69: NewChiralTestNoChiral +69: +69: Test +69: +69: NewChiralTestNoChiral +69: +69: Test +69: +69: NewChiralTest2 +69: +69: Test +69: +69: NewChiralTest2 +69: +69: Test +69: +69: NewChiralTest2AllChiral +69: +69: Test +69: +69: NewChiralTest2AllChiral +69: +69: Test +69: +69: Vendor839 +69: +69: Test +69: +69: DoubleBondChain +69: +69: Test +69: +69: Na_Mg_Al_OH +69: +69: Test +69: +69: Pb +69: +69: Test +69: +69: O_Mg_Si +69: +69: Test +69: +69: SquiggleBond +69: +69: Test +69: +69: BigMacrocycle +69: +69: Test +69: +69: Smiles1 +69: + 71/235 Test #69: testMrvToMol ........................... Passed 2.33 sec +81: [15:23:08] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +81: [15:23:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +test 83 + Start 83: XYZFileParserCatchTest + +83: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +83: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +83: Test timeout computed to be: 1500 +81: [15:23:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +81: [15:23:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +82: Randomness seeded to: 2000095169 +82: =============================================================================== +82: All tests passed (95 assertions in 4 test cases) +82: + 72/235 Test #82: testPropertyLists ...................... Passed 0.05 sec +test 84 + Start 84: cdxmlParserCatchTest + +84: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +84: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +84: Test timeout computed to be: 1500 +83: Randomness seeded to: 1460572979 +83: =============================================================================== +83: All tests passed (100 assertions in 2 test cases) +83: + 73/235 Test #83: XYZFileParserCatchTest ................. Passed 0.07 sec +test 85 + Start 85: molfileStereoCatchTest + +85: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +85: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +85: Test timeout computed to be: 1500 +85: Randomness seeded to: 815005210 +85: [15:23:08] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [15:23:08] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [15:23:08] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +85: [15:23:08] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. 85: =============================================================================== 85: All tests passed (142 assertions in 6 test cases) 85: - 74/235 Test #85: molfileStereoCatchTest ................. Passed 0.08 sec + 74/235 Test #85: molfileStereoCatchTest ................. Passed 0.06 sec test 86 Start 86: connectTheDotsTest 86: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest 86: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 86: Test timeout computed to be: 1500 -84: Randomness seeded to: 1881000464 -84: [05:51:07] Invalid or missing fragment id from CDXML fragment, assigning new one... -84: [05:51:07] Explicit valence for atom # 3 N, 4, is greater than permitted -84: [05:51:07] CDXMLParser: failed sanitizing skipping fragment 32 -84: [05:51:07] Bad bond in CDXML skipping fragment 58... -84: [05:51:07] Invalid or missing fragment id from CDXML fragment, assigning new one... -84: [05:51:07] Bad bond in CDXML skipping fragment 58... -81: [05:51:07] ERROR: molecules without atoms cannot be exported to Maestro files. -81: [05:51:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -81: [05:51:07] ERROR: the mol cannot be kekulized, and will not be written to the output file. -81: [05:51:07] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -81: [05:51:07] WARNING: atom 1 in input Maestro file has atomic number '0', which is reserved for internal use, and not allowed in inputs. The atom will be ignored.[05:51:07] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -81: [05:51:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -81: [05:51:07] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -81: [05:51:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -86: Randomness seeded to: 3339915400 +84: Randomness seeded to: 2434238225 +84: [15:23:08] Invalid or missing fragment id from CDXML fragment, assigning new one... +84: [15:23:08] Explicit valence for atom # 3 N, 4, is greater than permitted +84: [15:23:08] CDXMLParser: failed sanitizing skipping fragment 32 +84: [15:23:08] Bad bond in CDXML skipping fragment 58... +84: [15:23:08] Invalid or missing fragment id from CDXML fragment, assigning new one... +84: [15:23:08] Bad bond in CDXML skipping fragment 58... +86: Randomness seeded to: 1425021582 86: =============================================================================== 86: All tests passed (8 assertions in 1 test case) 86: - 75/235 Test #86: connectTheDotsTest ..................... Passed 0.04 sec + 75/235 Test #86: connectTheDotsTest ..................... Passed 0.08 sec test 87 Start 87: v2MolSuppliers 87: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2MolSuppliers 87: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 87: Test timeout computed to be: 1500 -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] WARNING: not removing hydrogen atom without neighbors -84: [05:51:07] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. -29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -87: Randomness seeded to: 3734857459 +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +87: Randomness seeded to: 3820573748 87: =============================================================================== 87: All tests passed (12 assertions in 5 test cases) 87: - 76/235 Test #87: v2MolSuppliers ......................... Passed 0.07 sec + 76/235 Test #87: v2MolSuppliers ......................... Passed 0.05 sec test 88 Start 88: v2FileParsersCatchTest 88: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/v2FileParsersCatchTest 88: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 88: Test timeout computed to be: 1500 -84: [05:51:07] Incomplete atom labelling, cannot make bond -84: [05:51:07] Incomplete atom labelling, cannot make bond -88: Randomness seeded to: 1727570448 +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] WARNING: not removing hydrogen atom without neighbors +84: [15:23:08] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents reaction fragment 64603 not found in document. +88: Randomness seeded to: 3184513006 88: =============================================================================== 88: All tests passed (6 assertions in 1 test case) 88: - 77/235 Test #88: v2FileParsersCatchTest ................. Passed 0.04 sec + 77/235 Test #88: v2FileParsersCatchTest ................. Passed 0.05 sec test 89 Start 89: multithreadedSupplierCatchTest 89: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/multithreadedSupplierCatchTest 89: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 89: Test timeout computed to be: 1500 -70: [05:51:07] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -70: [05:51:07] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -41: [05:51:07] done: 500000 -41: [05:51:07] Done -84: [05:51:07] Incomplete atom labelling, cannot make bond -84: [05:51:08] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -84: [05:51:08] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -84: [05:51:08] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -84: [05:51:08] Failed to parse XML fragment 5 node: b attribute: Order: 5 -41: [05:51:08] Testing hanoi with a functor. -84: [05:51:08] Invalid or missing fragment id from CDXML fragment, assigning new one... +84: [15:23:08] Incomplete atom labelling, cannot make bond +84: [15:23:08] Incomplete atom labelling, cannot make bond +84: [15:23:08] Incomplete atom labelling, cannot make bond +70: [15:23:08] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +70: [15:23:08] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +84: [15:23:08] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +84: [15:23:08] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +84: [15:23:08] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +84: [15:23:08] Failed to parse XML fragment 5 node: b attribute: Order: 5 +84: [15:23:08] Invalid or missing fragment id from CDXML fragment, assigning new one... 84: =============================================================================== 84: All tests passed (263 assertions in 7 test cases) 84: - 78/235 Test #84: cdxmlParserCatchTest ................... Passed 0.33 sec + 78/235 Test #84: cdxmlParserCatchTest ................... Passed 0.36 sec test 90 Start 90: testSubstructMatch 90: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 90: Test timeout computed to be: 1500 -41: [05:51:08] Done -41: [05:51:08] Testing basic partition refinement. -41: [05:51:08] Done -41: [05:51:08] Testing partition refinement with neighbors. -41: [05:51:08] Done -41: [05:51:08] testing canonicalization via tie breaking. -41: [05:51:08] Done -41: [05:51:08] testing canonicalization using the wrapper. -41: [05:51:08] Done -41: [05:51:08] testing some specific ordering problems -41: [05:51:08] Finished -41: [05:51:08] testing chiral invariants. -41: [05:51:08] Finished -41: [05:51:08] testing unique ranks in w.r.t. renumbering. 90: ----------------- Test 1 90: Done 90: @@ -22268,43 +22308,33 @@ 90: ----------------- Testing serial numbers on recursive queries 90: Done 90: -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test multithreading +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test multithreading 90: reading molecules +70: [15:23:09] Empty atom list: 'M ALS 1 0 F' on line 8. 90: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing 90: launch :0 90: launch :1 90: launch :2 90: launch :3 -70: ---------------------------------- -70: ---------------------------------- -70: [05:51:08] -70: -70: **** -70: Pre-condition Violation -70: rlabel out of range for MDL files -70: Violation occurred on line 857 in file ./Code/GraphMol/Atom.cpp -70: Failed Expression: rlabel >= 0 && rlabel < 100 -70: ---------- -70: Stacktrace: -70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -70: 3# 0x0000AAAABF4AF2FC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 4# 0x0000AAAABF514BA4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 5# 0x0000AAAABF485CB8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 6# 0x0000FFFF97FC229C in /lib/aarch64-linux-gnu/libc.so.6 -70: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -70: 8# 0x0000AAAABF485EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: ---------- -70: **** -70: -70: [05:51:08] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -41: [05:51:08] Finished -41: [05:51:08] testing mol fragments. -41: [05:51:08] Finished -41: [05:51:08] testing protein round-tripping. +70: de_DE.UTF-8 +70: [15:23:09] ------------------------------------- +70: [15:23:09] Test multithreading Locale Switching +70: [15:23:09] Test multithreading (Done) +70: [15:23:09] ------------------------------------- +70: *************************************** +70: *************************************** +70: [15:23:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [15:23:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +70: [15:23:09] bond with order 0 found on line 7. This is not part of the MDL specification. +70: [15:23:09] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +70: [15:23:09] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +70: [15:23:09] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +70: generating smiles +70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +70: converting back +70: check isomorphism 90: done 90: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 90: processing2 @@ -22320,37 +22350,194 @@ 90: launch3 :1 90: launch3 :2 90: launch3 :3 +89: Randomness seeded to: 3044199220 +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: done -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test GitHub issue 15 -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test GitHub issue 409 -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test chiral matching -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test dative-bond matching -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test cis/trans matching -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test cis/trans matching part 2 -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -90: [05:51:08] done -90: [05:51:08] ------------------------------------- -90: [05:51:08] Testing matching E/Z against Cis/Trans stereo bonds -90: [05:51:08] +90: [15:23:09] done +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test GitHub issue 15 +90: [15:23:09] done +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test GitHub issue 409 +90: [15:23:09] done +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test chiral matching +41: [15:23:09] done: 500000 +41: [15:23:09] Done +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [15:23:09] done +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +90: [15:23:09] done +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test dative-bond matching +90: [15:23:09] done +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test cis/trans matching +90: [15:23:09] done +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test cis/trans matching part 2 +90: [15:23:09] done +90: [15:23:09] ------------------------------------- +90: [15:23:09] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +90: [15:23:09] done +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +90: [15:23:09] ------------------------------------- +90: [15:23:09] Testing matching E/Z against Cis/Trans stereo bonds +90: [15:23:09] 90: 90: **** +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. 90: Pre-condition Violation 90: matches must not be empty 90: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp @@ -22361,15 +22548,15 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::getMostSubstitutedCoreMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAADACDAED0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAADACC9AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFFB46B229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAC5E4AED0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAC5E39AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFFBA3F229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAADACC9CF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAC5E39CF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [05:51:08] +90: [15:23:09] 90: 90: **** 90: Pre-condition Violation @@ -22382,539 +22569,307 @@ 90: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 90: 2# RDKit::detail::ScoreMatchesByDegreeOfCoreSubstitution::ScoreMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 90: 3# RDKit::sortMatchesByDegreeOfCoreSubstitution(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -90: 4# 0x0000AAAADACDB520 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 5# 0x0000AAAADACC9AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -90: 6# 0x0000FFFFB46B229C in /lib/aarch64-linux-gnu/libc.so.6 +90: 4# 0x0000AAAAC5E4B520 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 5# 0x0000AAAAC5E39AE8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 6# 0x0000FFFFBA3F229C in /lib/aarch64-linux-gnu/libc.so.6 90: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -90: 8# 0x0000AAAADACC9CF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +90: 8# 0x0000AAAAC5E39CF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 90: ---------- 90: **** 90: -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test substructure matching with a pathological case for symmetric SSSR -90: [05:51:08] ------------------------------------- -90: [05:51:08] Test isAtomTerminalRGroupOrQueryHydrogen - 79/235 Test #90: testSubstructMatch ..................... Passed 0.38 sec +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test substructure matching with a pathological case for symmetric SSSR +90: [15:23:09] ------------------------------------- +90: [15:23:09] Test isAtomTerminalRGroupOrQueryHydrogen +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 79/235 Test #90: testSubstructMatch ..................... Passed 0.55 sec test 91 Start 91: substructTestCatch 91: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch 91: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 91: Test timeout computed to be: 1500 -70: [05:51:08] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -70: [05:51:08] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -70: [05:51:08] Empty atom list: 'M ALS 1 0 F' on line 8. -41: [05:51:08] Finished -41: [05:51:08] testing stability w.r.t. renumbering. -70: de_DE.UTF-8 -70: [05:51:08] ------------------------------------- -70: [05:51:08] Test multithreading Locale Switching -41: [05:51:08] Finished -41: [05:51:08] testing smiles round-tripping. -89: Randomness seeded to: 83441556 -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: [05:51:08] Test multithreading (Done) -70: [05:51:08] ------------------------------------- -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: *************************************** -70: *************************************** -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: [05:51:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -70: [05:51:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: [05:51:08] bond with order 0 found on line 7. This is not part of the MDL specification. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 4.101s -12: -12: OK -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: [05:51:08] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -70: [05:51:08] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -70: [05:51:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -70: generating smiles -70: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -70: converting back -70: check isomorphism -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -91: Randomness seeded to: 3012959884 +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +89: [15:23:09] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. +41: [15:23:09] Testing hanoi with a functor. +41: [15:23:09] Done +41: [15:23:09] Testing basic partition refinement. +41: [15:23:09] Done +41: [15:23:09] Testing partition refinement with neighbors. +41: [15:23:09] Done +41: [15:23:09] testing canonicalization via tie breaking. +41: [15:23:09] Done +41: [15:23:09] testing canonicalization using the wrapper. +41: [15:23:09] Done +41: [15:23:09] testing some specific ordering problems +41: [15:23:09] Finished +41: [15:23:09] testing chiral invariants. +41: [15:23:09] Finished +41: [15:23:09] testing unique ranks in w.r.t. renumbering. +41: [15:23:09] Finished +41: [15:23:09] testing mol fragments. +41: [15:23:09] Finished +41: [15:23:09] testing protein round-tripping. +89: [15:23:10] Explicit valence for atom # 9 N, 6, is greater than permitted +91: Randomness seeded to: 1879666331 91: =============================================================================== 91: All tests passed (242 assertions in 12 test cases) 91: -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. - 80/235 Test #91: substructTestCatch ..................... Passed 0.48 sec -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. + 80/235 Test #91: substructTestCatch ..................... Passed 0.59 sec test 92 Start 92: testGenericGroups 92: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 92: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups 92: Test timeout computed to be: 1500 -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. -89: [05:51:08] Read callback exception: I'm Sorry Dave. I'm afraid I can't do that. - 81/235 Test #12: pyBV ................................... Passed 4.76 sec +12: .................. +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 6.099s +12: +12: OK +89: [15:23:10] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [15:23:10] Explicit valence for atom # 4 Al, 6, is greater than permitted + 81/235 Test #12: pyBV ................................... Passed 7.43 sec test 93 Start 93: testReaction 93: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 93: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 93: Test timeout computed to be: 1500 -41: [05:51:08] Finished -41: [05:51:08] testing github #1567: Non-canonical result from MolFragmentToSmiles() -41: [05:51:08] Finished - 82/235 Test #41: hanoiTest .............................. Passed 3.76 sec -test 94 - Start 94: testReactionFingerprints - -94: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -94: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -94: Test timeout computed to be: 1500 +89: [15:23:10] Explicit valence for atom # 10 Si, 6, is greater than permitted 93: smi: O=C1CNC(=O)CN1 93: 1: O=C1CNC(=O)CN1 93: 2: COOC -93: [05:51:08] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [05:51:08] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 93: O=C1CNC(=O)CN1 -93: [05:51:08] product atom-mapping number 1 found multiple times. -93: [05:51:08] mapped atoms in the reactants were not mapped in the products. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -94: [05:51:08] ------------------------------------- -94: [05:51:08] Test Reaction StructuralFingerprint -93: [05:51:08] atom 0 in product 0 has multiple charge specifications. +93: [15:23:10] atom 0 in product 0 has multiple charge specifications. 93: mass: 15.0001 93: Oc1ccccn1 93: Oc1ccc[nH]1 -93: [05:51:09] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -93: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -93: [05:51:09] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [05:51:09] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -93: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -93: [05:51:09] SMARTS Parse Error: syntax error while parsing: [C:2]) -93: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -93: [05:51:09] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -93: [05:51:09] SMILES Parse Error: check for mistakes around position 2: -93: [05:51:09] [Q:1][C:2][C:3](=[O:4])[O:5] -93: [05:51:09] ~^ -93: [05:51:09] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -93: [05:51:09] reactant 2 has no mapped atoms. -93: [05:51:09] >> Atoms within one molecule have different RXN roles. -94: [05:51:09] ------------------------------------- -94: [05:51:09] Test Reaction DifferenceFingerprint - 83/235 Test #94: testReactionFingerprints ............... Passed 0.08 sec -test 95 - Start 95: testEnumeration - -95: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -95: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -95: Test timeout computed to be: 1500 -93: [05:51:09] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -93: [05:51:09] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -93: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -93: [05:51:09] SMARTS Parse Error: syntax error while parsing: ([C:2] -93: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -93: [05:51:09] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -93: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -93: [05:51:09] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -93: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -93: [05:51:09] reactant 0 has no mapped atoms. -93: [05:51:09] reactant 1 has no mapped atoms. -93: [05:51:09] reactant 3 has no mapped atoms. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 5 found multiple times. -93: [05:51:09] product atom-mapping number 6 found multiple times. -93: [05:51:09] product atom-mapping number 7 found multiple times. -93: [05:51:09] product atom-mapping number 8 found multiple times. -93: [05:51:09] product atom-mapping number 12 found multiple times. -93: [05:51:09] product atom-mapping number 9 found multiple times. -93: [05:51:09] product atom-mapping number 10 found multiple times. -93: [05:51:09] product atom-mapping number 11 found multiple times. -93: [05:51:09] reactant 0 has no mapped atoms. -93: [05:51:09] reactant 1 has no mapped atoms. -93: [05:51:09] reactant 3 has no mapped atoms. -93: [05:51:09] reactant atom-mapping number 19 found multiple times. -93: [05:51:09] reactant atom-mapping number 25 found multiple times. -93: [05:51:09] reactant atom-mapping number 20 found multiple times. -93: [05:51:09] reactant atom-mapping number 21 found multiple times. -93: [05:51:09] reactant atom-mapping number 22 found multiple times. -93: [05:51:09] reactant atom-mapping number 23 found multiple times. -93: [05:51:09] reactant atom-mapping number 24 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. +41: [15:23:10] Finished +41: [15:23:10] testing stability w.r.t. renumbering. +89: [15:23:10] Explicit valence for atom # 2 O, 4, is greater than permitted +89: [15:23:10] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [15:23:10] Explicit valence for atom # 3 Be, 4, is greater than permitted +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [C:2]) +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +93: [15:23:10] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +93: [15:23:10] SMILES Parse Error: check for mistakes around position 2: +93: [15:23:10] [Q:1][C:2][C:3](=[O:4])[O:5] +93: [15:23:10] ~^ +93: [15:23:10] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +93: [15:23:10] reactant 2 has no mapped atoms. +89: [15:23:10] Explicit valence for atom # 27 P, 6, is greater than permitted +41: [15:23:10] Finished +41: [15:23:10] testing smiles round-tripping. +93: [15:23:10] >> Atoms within one molecule have different RXN roles. +93: [15:23:10] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: ([C:2] +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +93: [15:23:10] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +93: [15:23:10] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +93: [15:23:10] reactant 0 has no mapped atoms. +93: [15:23:10] reactant 1 has no mapped atoms. +93: [15:23:10] reactant 3 has no mapped atoms. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 5 found multiple times. +93: [15:23:10] product atom-mapping number 6 found multiple times. +93: [15:23:10] product atom-mapping number 7 found multiple times. +93: [15:23:10] product atom-mapping number 8 found multiple times. +93: [15:23:10] product atom-mapping number 12 found multiple times. +93: [15:23:10] product atom-mapping number 9 found multiple times. +93: [15:23:10] product atom-mapping number 10 found multiple times. +93: [15:23:10] product atom-mapping number 11 found multiple times. +93: [15:23:10] reactant 0 has no mapped atoms. +93: [15:23:10] reactant 1 has no mapped atoms. +93: [15:23:10] reactant 3 has no mapped atoms. +93: [15:23:10] reactant atom-mapping number 19 found multiple times. +93: [15:23:10] reactant atom-mapping number 25 found multiple times. +93: [15:23:10] reactant atom-mapping number 20 found multiple times. +93: [15:23:10] reactant atom-mapping number 21 found multiple times. +93: [15:23:10] reactant atom-mapping number 22 found multiple times. +93: [15:23:10] reactant atom-mapping number 23 found multiple times. +93: [15:23:10] reactant atom-mapping number 24 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [05:51:09] product atom-mapping number 5 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 5 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 5 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 5 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [05:51:09] product atom-mapping number 5 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 5 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 5 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 5 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. 93: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. 93: F[C@](Cl)(Br)O[C@](F)(Cl)Br -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 4 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] mapped atoms in the reactants were not mapped in the products. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 4 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [05:51:09] product atom-mapping number 3 found multiple times. -93: [05:51:09] product atom-mapping number 2 found multiple times. -93: [05:51:09] product atom-mapping number 1 found multiple times. -93: [05:51:09] mapped atoms in the reactants were not mapped in the products. +93: [15:23:10] product atom-mapping number 3 found multiple times. +93: [15:23:10] product atom-mapping number 2 found multiple times. +93: [15:23:10] product atom-mapping number 1 found multiple times. +93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 4 -93: [05:51:09] product atom-mapping number 6 not found in reactants. -93: [05:51:09] product atom-mapping number 7 not found in reactants. -93: [05:51:09] product atom-mapping number 8 not found in reactants. -93: [05:51:09] product atom-mapping number 7 not found in reactants. -93: [05:51:09] product atom-mapping number 8 not found in reactants. -93: [05:51:09] product atom-mapping number 9 not found in reactants. -93: [05:51:09] product atom-mapping number 10 not found in reactants. -93: [05:51:09] mapped atoms in the reactants were not mapped in the products. +93: [15:23:10] product atom-mapping number 6 not found in reactants. +93: [15:23:10] product atom-mapping number 7 not found in reactants. +93: [15:23:10] product atom-mapping number 8 not found in reactants. +93: [15:23:10] product atom-mapping number 7 not found in reactants. +93: [15:23:10] product atom-mapping number 8 not found in reactants. +93: [15:23:10] product atom-mapping number 9 not found in reactants. +93: [15:23:10] product atom-mapping number 10 not found in reactants. +93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 -93: [05:51:09] product atom-mapping number 7 not found in reactants. -93: [05:51:09] product atom-mapping number 8 not found in reactants. -93: [05:51:09] product atom-mapping number 9 not found in reactants. -93: [05:51:09] product atom-mapping number 10 not found in reactants. -93: [05:51:09] mapped atoms in the reactants were not mapped in the products. +93: [15:23:10] product atom-mapping number 7 not found in reactants. +93: [15:23:10] product atom-mapping number 8 not found in reactants. +93: [15:23:10] product atom-mapping number 9 not found in reactants. +93: [15:23:10] product atom-mapping number 10 not found in reactants. +93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 6 93: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 93: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -93: [05:51:09] mapped atoms in the reactants were not mapped in the products. +93: [15:23:10] mapped atoms in the reactants were not mapped in the products. 93: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -93: [05:51:09] product atom-mapping number 17 not found in reactants. -93: [05:51:09] product atom-mapping number 18 not found in reactants. -93: [05:51:09] mapped atoms in the reactants were not mapped in the products. -93: unmapped numbers are: 12 -93: [05:51:09] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: [05:51:09] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -93: -93: [05:51:09] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -93: ------------- -93: CCOc1ccccc1 -95: 30000000 30000000 -93: [05:51:09] reactant 0 has no mapped atoms. -93: [05:51:09] product 0 has no mapped atoms. -93: [05:51:09] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. - 84/235 Test #93: testReaction ........................... Passed 0.42 sec -test 96 - Start 96: rxnTestCatch - -96: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch -96: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -96: Test timeout computed to be: 1500 -92: Randomness seeded to: 457396480 -92: =============================================================================== -92: All tests passed (11480 assertions in 38 test cases) -92: - 85/235 Test #92: testGenericGroups ...................... Passed 0.48 sec -test 97 - Start 97: pyChemReactions - -97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" -97: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -97: Test timeout computed to be: 1500 -96: Randomness seeded to: 690442633 -96: [05:51:09] atom 0 in product 0 has multiple charge specifications. -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 34 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 36 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 38 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 40 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 42 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 87 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 89 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 91 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 93 -96: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 95 -96: [05:51:09] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [05:51:09] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [05:51:09] SMARTS Parse Error: unclosed ring for input: 'CC1' -96: [05:51:09] SMILES Parse Error: unclosed ring for input: 'CC1' -96: [05:51:09] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [05:51:09] product atom-mapping number 2 not found in reactants. -96: [05:51:09] mapped atoms in the reactants were not mapped in the products. -96: unmapped numbers are: 2 -96: [05:51:09] product atom-mapping number 2 not found in reactants. -96: [05:51:09] CX Extensions: Substance group hierarchy is not always preserved. -96: [05:51:09] CX Extensions: Substance group hierarchy is not always preserved. -96: [05:51:09] reactant 0 has no mapped atoms. -96: [05:51:09] product 0 has no mapped atoms. -96: [05:51:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [05:51:09] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -96: [05:51:09] Explicit valence for atom # 1 O, 5, is greater than permitted -96: =============================================================================== -96: All tests passed (722 assertions in 30 test cases) -96: - 86/235 Test #96: rxnTestCatch ........................... Passed 0.12 sec -test 98 - Start 98: pyChemReactionEnumerations +41: [15:23:10] Finished +41: [15:23:10] testing github #1567: Non-canonical result from MolFragmentToSmiles() +41: [15:23:10] Finished +70: [15:23:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [15:23:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [15:23:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [15:23:10] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +70: [15:23:10] deprecated group abbreviation ignored on line 24 + 82/235 Test #41: hanoiTest .............................. Passed 5.69 sec +test 94 + Start 94: testReactionFingerprints -98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" -98: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -98: Test timeout computed to be: 1500 -70: [05:51:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [05:51:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [05:51:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [05:51:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -70: [05:51:09] deprecated group abbreviation ignored on line 24 +94: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +94: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +94: Test timeout computed to be: 1500 70: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -70: [05:51:09] +70: [15:23:10] 70: 70: **** 70: Post-condition Violation @@ -22926,241 +22881,47 @@ 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 2# RDKit::PeriodicTable::getAtomicNumber(std::__cxx11::basic_string, std::allocator > const&) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 3# 0x0000FFFF988F7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 4# 0x0000FFFF98905BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 5# 0x0000FFFF98906AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 3# 0x0000FFFFB8CA7FE4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 4# 0x0000FFFFB8CB5BC0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 +70: 5# 0x0000FFFFB8CB6AEC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 6# RDKit::FileParserUtils::ParseV2000CTAB(std::istream*, unsigned int&, RDKit::RWMol*, RDKit::Conformer*&, bool&, unsigned int&, unsigned int&, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 7# RDKit::v2::FileParsers::MolFromMolDataStream(std::istream&, unsigned int&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 70: 8# RDKit::v2::FileParsers::MolFromMolFile(std::__cxx11::basic_string, std::allocator > const&, RDKit::v2::FileParsers::MolFileParserParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFileParsers.so.1 -70: 9# 0x0000AAAABF49F83C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 10# 0x0000AAAABF514B44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 11# 0x0000AAAABF485D2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 12# 0x0000FFFF97FC229C in /lib/aarch64-linux-gnu/libc.so.6 +70: 9# 0x0000AAAAC525F83C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 10# 0x0000AAAAC52D4B44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 11# 0x0000AAAAC5245D2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 12# 0x0000FFFFB837229C in /lib/aarch64-linux-gnu/libc.so.6 70: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -70: 14# 0x0000AAAABF485EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 14# 0x0000AAAAC5245EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: - 87/235 Test #43: resMolSupplierTest ..................... Passed 4.62 sec -test 99 - Start 99: pyChemReactionSanitize +93: [15:23:10] product atom-mapping number 17 not found in reactants. +93: [15:23:10] product atom-mapping number 18 not found in reactants. +93: [15:23:10] mapped atoms in the reactants were not mapped in the products. +93: unmapped numbers are: 12 +94: [15:23:10] ------------------------------------- +94: [15:23:10] Test Reaction StructuralFingerprint +93: [15:23:10] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: [15:23:10] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +93: +93: [15:23:10] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +93: ------------- +93: CCOc1ccccc1 +94: [15:23:10] ------------------------------------- +94: [15:23:10] Test Reaction DifferenceFingerprint + 83/235 Test #94: testReactionFingerprints ............... Passed 0.14 sec +test 95 + Start 95: testEnumeration -99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" -99: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -99: Test timeout computed to be: 1500 -97: ...[05:51:09] -97: -97: **** -70: [05:51:09] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -70: [05:51:09] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -98: [05:51:09] == testCartesianProduct -97: Pre-condition Violation -97: getNumImplicitHs() called without preceding call to calcImplicitValence() -97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp -97: Failed Expression: d_implicitValence > -1 -97: ---------- -97: Stacktrace: -97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x0000FFFF84702680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF82D0B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF82D0B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF82D0B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF82D0B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF82D0B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x0000FFFF846FF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 47# _PyObject_MakeTpCall in /usr/bin/python3 -97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 49# 0x00000000005335D0 in /usr/bin/python3 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x00000000004AC3B4 in /usr/bin/python3 -97: 52# 0x0000000000665934 in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x00000000005335D0 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x00000000004AC3B4 in /usr/bin/python3 -97: 58# 0x0000000000665934 in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x00000000005335D0 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x00000000004AC3B4 in /usr/bin/python3 -97: 64# 0x0000000000665934 in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x00000000005051B0 in /usr/bin/python3 -97: 68# _PyObject_MakeTpCall in /usr/bin/python3 -97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 70# PyEval_EvalCode in /usr/bin/python3 -97: 71# 0x00000000005FFD24 in /usr/bin/python3 -97: 72# 0x00000000005F9904 in /usr/bin/python3 -97: 73# 0x0000000000627ED4 in /usr/bin/python3 -97: 74# 0x0000000000627274 in /usr/bin/python3 -97: 75# 0x0000000000627010 in /usr/bin/python3 -97: 76# Py_RunMain in /usr/bin/python3 -97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF8523229C in /lib/aarch64-linux-gnu/libc.so.6 -97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -97: 80# _start in /usr/bin/python3 -97: ---------- -97: **** -97: -97: [05:51:09] -97: -97: **** -97: Pre-condition Violation -97: getNumImplicitHs() called without preceding call to calcImplicitValence() -97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp -97: Failed Expression: d_implicitValence > -1 -97: ---------- -97: Stacktrace: -97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 -97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 25# 0x0000FFFF84702680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so -97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so -97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so -97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so -97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 36# 0x0000FFFF82D0B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 37# 0x0000FFFF82D0B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 38# 0x0000FFFF82D0B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 39# 0x0000FFFF82D0B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 40# 0x0000FFFF82D0B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 46# 0x0000FFFF846FF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -97: 47# _PyObject_MakeTpCall in /usr/bin/python3 -97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 49# 0x00000000005335D0 in /usr/bin/python3 -97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 51# 0x00000000004AC3B4 in /usr/bin/python3 -97: 52# 0x0000000000665934 in /usr/bin/python3 -97: 53# _PyObject_MakeTpCall in /usr/bin/python3 -97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 55# 0x00000000005335D0 in /usr/bin/python3 -97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 57# 0x00000000004AC3B4 in /usr/bin/python3 -97: 58# 0x0000000000665934 in /usr/bin/python3 -97: 59# _PyObject_MakeTpCall in /usr/bin/python3 -97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 61# 0x00000000005335D0 in /usr/bin/python3 -97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 63# 0x00000000004AC3B4 in /usr/bin/python3 -97: 64# 0x0000000000665934 in /usr/bin/python3 -97: 65# _PyObject_MakeTpCall in /usr/bin/python3 -97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 67# 0x00000000005051B0 in /usr/bin/python3 -97: 68# _PyObject_MakeTpCall in /usr/bin/python3 -97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 -97: 70# PyEval_EvalCode in /usr/bin/python3 -97: 71# 0x00000000005FFD24 in /usr/bin/python3 -97: 72# 0x00000000005F9904 in /usr/bin/python3 -97: 73# 0x0000000000627ED4 in /usr/bin/python3 -97: 74# 0x0000000000627274 in /usr/bin/python3 -97: 75# 0x0000000000627010 in /usr/bin/python3 -97: 76# Py_RunMain in /usr/bin/python3 -97: 77# Py_BytesMain in /usr/bin/python3 -97: 78# 0x0000FFFF8523229C in /lib/aarch64-linux-gnu/libc.so.6 -97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -97: 80# _start in /usr/bin/python3 -97: ---------- -97: **** -97: -98: .[05:51:09] == testEnumerateLibrary -98: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -98: ResourceWarning: Enable tracemalloc to get the object allocation traceback -97: .........[05:51:09] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [05:51:09] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [05:51:09] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: [05:51:09] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -97: .[05:51:09] product atom-mapping number 1 found multiple times. -97: [05:51:09] product atom-mapping number 1 found multiple times. -97: ................[05:51:09] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: [05:51:09] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -97: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -97: [05:51:09] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 3 -97: ..[05:51:09] reactant 2 has no mapped atoms. -97: [05:51:09] reactant 2 has no mapped atoms. -97: [05:51:09] product 1 has no mapped atoms. +95: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +95: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +95: Test timeout computed to be: 1500 +70: [15:23:10] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +70: [15:23:10] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 70: ---------------------------------- 70: ---------------------------------- -70: [05:51:09] +70: [15:23:10] 70: 70: **** 70: Pre-condition Violation @@ -23172,218 +22933,153 @@ 70: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 70: 2# RDKit::setAtomRLabel(RDKit::Atom*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -70: 3# 0x0000AAAABF4AF2FC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 4# 0x0000AAAABF514BA4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 5# 0x0000AAAABF485D2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -70: 6# 0x0000FFFF97FC229C in /lib/aarch64-linux-gnu/libc.so.6 +70: 3# 0x0000AAAAC526F2FC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 4# 0x0000AAAAC52D4BA4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 5# 0x0000AAAAC5245D2C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 6# 0x0000FFFFB837229C in /lib/aarch64-linux-gnu/libc.so.6 70: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -70: 8# 0x0000AAAABF485EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +70: 8# 0x0000AAAAC5245EF0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 70: ---------- 70: **** 70: -70: [05:51:09] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -97: ........[05:51:09] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -97: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -97: [05:51:09] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -97: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -97: .[05:51:09] reactant atom-mapping number 1 found multiple times. -97: [05:51:09] product atom-mapping number 2 not found in reactants. -97: [05:51:09] mapped atoms in the reactants were not mapped in the products. -97: unmapped numbers are: 4 -97: [05:51:09] product atom-mapping number 5 not found in reactants. -98: ..[05:51:09] == testRGroupState -98: .[05:51:09] == testRandomEnumerateAllBBsLibrary -98: ** [1, 1] -98: ** [0, 2] -98: ** [1, 0] -97: ........./build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -97: png = open(fname, 'rb').read() -97: ResourceWarning: Enable tracemalloc to get the object allocation traceback -98: .[05:51:09] == testRandomEnumerateLibrary -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 34 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 36 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 38 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 40 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 42 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 87 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 89 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 91 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 93 -97: [05:51:09] Found a SCD/SED line with missing/empty SDT specification at line 95 -98: .[05:51:09] == testRandomSample -97: ..[05:51:09] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [05:51:09] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -98: .[05:51:10] == testRandomSampleAllBBs -97: [05:51:10] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [05:51:10] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [05:51:10] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [05:51:10] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [05:51:10] reaction has no reactants -97: [05:51:10] reaction has no products -97: [05:51:10] initialization failed -97: [05:51:10] reaction has no reactants -97: [05:51:10] reaction has no products -98: .[05:51:10] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: [05:51:10] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -98: .[05:51:10] == testRemoveBadMatches -98: .[05:51:10] == testTimings -97: .[05:51:10] SMARTS Parse Error: syntax error while parsing: boromicacid -97: [05:51:10] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -97: [05:51:10] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -97: [05:51:10] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -97: [05:51:10] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -97: [05:51:10] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -97: [05:51:10] reaction has no reactants -97: [05:51:10] reaction has no products -97: [05:51:10] initialization failed -97: [05:51:10] reaction has no reactants -97: [05:51:10] reaction has no products -97: . -97: ---------------------------------------------------------------------- -97: Ran 54 tests in 0.209s -97: -97: OK -97: ******************************************** -97: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -97: - 88/235 Test #97: pyChemReactions ........................ Passed 0.77 sec -test 100 - Start 100: testChemTransforms +92: Randomness seeded to: 2909242045 +92: =============================================================================== +92: All tests passed (11480 assertions in 38 test cases) +92: + 84/235 Test #92: testGenericGroups ...................... Passed 0.65 sec +test 96 + Start 96: rxnTestCatch -100: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms -100: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms -100: Test timeout computed to be: 1500 -89: [05:51:10] Explicit valence for atom # 9 N, 6, is greater than permitted -70: [05:51:10] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -70: [05:51:10] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -100: 1 smi: CC -100: 1 smi: CC -100: 2 smi: CCO[C@H](N)P -100: 2 smi: CC -100: replaceSub smi1:CCP(CC)[C@@H](N)O -100: replaceSub smi1:CCNCC -100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O -100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -100: [05:51:10] SMARTS Parse Error: syntax error while parsing: bar -100: [05:51:10] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -70: [05:51:10] Empty atom list: 'M ALS 1 0 F' on line 8. - 89/235 Test #70: fileParsersTest1 ....................... Passed 3.86 sec -test 101 - Start 101: chemTransformsTestCatch +96: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch +96: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +96: Test timeout computed to be: 1500 +70: [15:23:10] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +95: 30000000 30000000 +96: Randomness seeded to: 1199136542 +96: [15:23:10] atom 0 in product 0 has multiple charge specifications. +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 34 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 36 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 38 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 40 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 42 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 87 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 89 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 91 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 93 +96: [15:23:10] Found a SCD/SED line with missing/empty SDT specification at line 95 +96: [15:23:10] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [15:23:10] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [15:23:10] SMARTS Parse Error: unclosed ring for input: 'CC1' +96: [15:23:10] SMILES Parse Error: unclosed ring for input: 'CC1' +96: [15:23:10] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [15:23:10] product atom-mapping number 2 not found in reactants. +96: [15:23:10] mapped atoms in the reactants were not mapped in the products. +96: unmapped numbers are: 2 +96: [15:23:10] product atom-mapping number 2 not found in reactants. +96: [15:23:10] CX Extensions: Substance group hierarchy is not always preserved. +96: [15:23:10] CX Extensions: Substance group hierarchy is not always preserved. +93: [15:23:10] reactant 0 has no mapped atoms. +93: [15:23:10] product 0 has no mapped atoms. +93: [15:23:10] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. +96: [15:23:10] reactant 0 has no mapped atoms. +96: [15:23:10] product 0 has no mapped atoms. +96: [15:23:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [15:23:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +96: [15:23:10] Explicit valence for atom # 1 O, 5, is greater than permitted + 85/235 Test #93: testReaction ........................... Passed 0.65 sec +test 97 + Start 97: pyChemReactions -101: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms -101: Test timeout computed to be: 1500 - 90/235 Test #100: testChemTransforms ..................... Passed 0.13 sec -test 102 - Start 102: tautomerQueryTestCatch +97: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" +97: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +97: Test timeout computed to be: 1500 +96: =============================================================================== +96: All tests passed (722 assertions in 30 test cases) +96: + 86/235 Test #96: rxnTestCatch ........................... Passed 0.11 sec +test 98 + Start 98: pyChemReactionEnumerations -102: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -102: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery -102: Test timeout computed to be: 1500 -89: [05:51:10] Explicit valence for atom # 3 Al, 6, is greater than permitted -101: Randomness seeded to: 794137466 -101: [05:51:10] Incomplete atom labelling, cannot make bond -101: [05:51:10] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAABE9E6F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAABEA350AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAABEA35A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAABEA35E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAABEA0A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAABEA0A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAABE9DC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFFA22D229C in /lib/aarch64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAABE9DC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -89: [05:51:10] Explicit valence for atom # 4 Al, 6, is greater than permitted -101: [05:51:10] Incomplete atom labelling, cannot make bond -101: [05:51:10] -101: -101: **** -101: Invariant Violation -101: molzip: bond info already exists for end atom with label:1 -101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -101: Failed Expression: !bond.b -101: ---------- -101: Stacktrace: -101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAABE9E6F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAABEA350AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAABEA35A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAABEA35E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAABEA0A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAABEA0A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAABE9DC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFFA22D229C in /lib/aarch64-linux-gnu/libc.so.6 -101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAABE9DC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: ---------- -101: **** -101: -99: .[05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: .[05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. +98: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" +98: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +98: Test timeout computed to be: 1500 +89: [15:23:10] Explicit valence for atom # 9 N, 6, is greater than permitted +70: [15:23:11] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +70: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +29: All 191 tests passed +70: [15:23:11] Empty atom list: 'M ALS 1 0 F' on line 8. + 87/235 Test #70: fileParsersTest1 ....................... Passed 4.77 sec +test 99 + Start 99: pyChemReactionSanitize + +99: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" +99: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +99: Test timeout computed to be: 1500 +89: [15:23:11] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [15:23:11] Explicit valence for atom # 4 Al, 6, is greater than permitted +89: [15:23:11] Explicit valence for atom # 10 Si, 6, is greater than permitted +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +89: [15:23:11] Explicit valence for atom # 2 O, 4, is greater than permitted +98: [15:23:11] == testCartesianProduct +99: .[15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +98: .[15:23:11] == testEnumerateLibrary +97: ...[15:23:11] +97: +97: **** +98: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +98: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +98: ResourceWarning: Enable tracemalloc to get the object allocation traceback +89: [15:23:11] Explicit valence for atom # 3 Al, 6, is greater than permitted +89: [15:23:11] Explicit valence for atom # 3 Be, 4, is greater than permitted +99: .[15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. 99: () 99: ******************************************** 99: $RXN @@ -23747,16 +23443,16 @@ 99: 1 2 1 0 99: M ISO 2 1 1 2 2 99: M END -99: [05:51:10] reactant 0 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] product 0 has no mapped atoms. -99: [05:51:10] Could not find RLabel mapping for atom: 0 in template: 1 -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. -99: [05:51:10] reactant 1 has no mapped atoms. +99: [15:23:11] reactant 0 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] product 0 has no mapped atoms. +99: [15:23:11] Could not find RLabel mapping for atom: 0 in template: 1 +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. +99: [15:23:11] reactant 1 has no mapped atoms. 99: .. 99: ---------------------------------------------------------------------- -99: Ran 4 tests in 0.029s +99: Ran 4 tests in 0.060s 99: 99: OK 99: @@ -23813,8 +23509,369 @@ 99: M END 99: 99: $RXN Failed -101: [05:51:10] Incomplete atom labelling, cannot make bond -101: [05:51:10] +97: Pre-condition Violation +97: getNumImplicitHs() called without preceding call to calcImplicitValence() +97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp +97: Failed Expression: d_implicitValence > -1 +97: ---------- +97: Stacktrace: +97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFF86F02680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFF8550B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFF8550B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFF8550B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFF8550B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFF8550B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFF86EFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 47# _PyObject_MakeTpCall in /usr/bin/python3 +97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 49# 0x00000000005335D0 in /usr/bin/python3 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x00000000004AC3B4 in /usr/bin/python3 +97: 52# 0x0000000000665934 in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x00000000005335D0 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x00000000004AC3B4 in /usr/bin/python3 +97: 58# 0x0000000000665934 in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x00000000005335D0 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x00000000004AC3B4 in /usr/bin/python3 +97: 64# 0x0000000000665934 in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x00000000005051B0 in /usr/bin/python3 +97: 68# _PyObject_MakeTpCall in /usr/bin/python3 +97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 70# PyEval_EvalCode in /usr/bin/python3 +97: 71# 0x00000000005FFD24 in /usr/bin/python3 +97: 72# 0x00000000005F9904 in /usr/bin/python3 +97: 73# 0x0000000000627ED4 in /usr/bin/python3 +97: 74# 0x0000000000627274 in /usr/bin/python3 +97: 75# 0x0000000000627010 in /usr/bin/python3 +97: 76# Py_RunMain in /usr/bin/python3 +97: 77# Py_BytesMain in /usr/bin/python3 +97: 78# 0x0000FFFF87A3229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +97: 80# _start in /usr/bin/python3 +97: ---------- +97: **** +97: +97: [15:23:11] +97: +97: **** +97: Pre-condition Violation +97: getNumImplicitHs() called without preceding call to calcImplicitValence() +97: Violation occurred on line 302 in file ./Code/GraphMol/Atom.cpp +97: Failed Expression: d_implicitValence > -1 +97: ---------- +97: Stacktrace: +97: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +97: 2# RDKit::Atom::getNumImplicitHs() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 3# RDKit::Atom::getTotalNumHs(bool) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 4# Queries::EqualityQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +97: 5# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 6# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 7# Queries::OrQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +97: 8# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 9# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 10# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 11# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 12# RDKit::detail::RecursiveMatcher(RDKit::ROMol const&, RDKit::ROMol const&, std::vector >&, std::map*, std::less, std::allocator*> > >&, RDKit::SubstructMatchParameters const&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 13# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 14# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 15# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 16# RDKit::detail::MatchSubqueries(RDKit::ROMol const&, Queries::Query*, RDKit::SubstructMatchParameters const&, std::map*, std::less, std::allocator*> > >&, std::vector >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 17# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +97: 18# RDKit::ReactionRunnerUtils::getReactantMatchesToTemplate(RDKit::ROMol const&, RDKit::ROMol const&, unsigned int, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 19# RDKit::ReactionRunnerUtils::getReactantMatches(std::vector, std::allocator > > const&, RDKit::ChemicalReaction const&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >, std::allocator, std::allocator > >, std::allocator, std::allocator > > > > > >&, unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 20# RDKit::run_Reactants(RDKit::ChemicalReaction const&, std::vector, std::allocator > > const&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 21# RDKit::ChemicalReaction::runReactants(std::vector, std::allocator > >, unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemReactions.so.1 +97: 22# _object* RDKit::RunReactants(RDKit::ChemicalReaction*, boost::python::tuple, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 23# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 24# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 25# 0x0000FFFF86F02680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 26# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so +97: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so +97: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 30# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so +97: 31# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolChemicalFeatures.so +97: 32# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 33# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +97: 34# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +97: 35# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 36# 0x0000FFFF8550B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 37# 0x0000FFFF8550B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 38# 0x0000FFFF8550B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 39# 0x0000FFFF8550B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 40# 0x0000FFFF8550B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +97: 41# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +97: 42# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +97: 43# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +97: 44# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +97: 45# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 46# 0x0000FFFF86EFF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +97: 47# _PyObject_MakeTpCall in /usr/bin/python3 +97: 48# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 49# 0x00000000005335D0 in /usr/bin/python3 +97: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 51# 0x00000000004AC3B4 in /usr/bin/python3 +97: 52# 0x0000000000665934 in /usr/bin/python3 +97: 53# _PyObject_MakeTpCall in /usr/bin/python3 +97: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 55# 0x00000000005335D0 in /usr/bin/python3 +97: 56# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 57# 0x00000000004AC3B4 in /usr/bin/python3 +97: 58# 0x0000000000665934 in /usr/bin/python3 +97: 59# _PyObject_MakeTpCall in /usr/bin/python3 +97: 60# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 61# 0x00000000005335D0 in /usr/bin/python3 +97: 62# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 63# 0x00000000004AC3B4 in /usr/bin/python3 +97: 64# 0x0000000000665934 in /usr/bin/python3 +97: 65# _PyObject_MakeTpCall in /usr/bin/python3 +97: 66# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 67# 0x00000000005051B0 in /usr/bin/python3 +97: 68# _PyObject_MakeTpCall in /usr/bin/python3 +97: 69# _PyEval_EvalFrameDefault in /usr/bin/python3 +97: 70# PyEval_EvalCode in /usr/bin/python3 +97: 71# 0x00000000005FFD24 in /usr/bin/python3 +97: 72# 0x00000000005F9904 in /usr/bin/python3 +97: 73# 0x0000000000627ED4 in /usr/bin/python3 +97: 74# 0x0000000000627274 in /usr/bin/python3 +97: 75# 0x0000000000627010 in /usr/bin/python3 +97: 76# Py_RunMain in /usr/bin/python3 +97: 77# Py_BytesMain in /usr/bin/python3 +97: 78# 0x0000FFFF87A3229C in /lib/aarch64-linux-gnu/libc.so.6 +97: 79# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +97: 80# _start in /usr/bin/python3 +97: ---------- +97: **** +97: + 88/235 Test #43: resMolSupplierTest ..................... Passed 7.04 sec +test 100 + Start 100: testChemTransforms + +100: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms +100: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms +100: Test timeout computed to be: 1500 +97: .........[15:23:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [15:23:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [15:23:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: [15:23:11] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +97: .[15:23:11] product atom-mapping number 1 found multiple times. +97: [15:23:11] product atom-mapping number 1 found multiple times. +97: ................[15:23:11] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: [15:23:11] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: .:488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. +97: [15:23:11] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 3 +97: ..[15:23:11] reactant 2 has no mapped atoms. +97: [15:23:11] reactant 2 has no mapped atoms. +97: [15:23:11] product 1 has no mapped atoms. +97: ........[15:23:11] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +97: [15:23:11] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +97: .[15:23:11] reactant atom-mapping number 1 found multiple times. +97: [15:23:11] product atom-mapping number 2 not found in reactants. +97: [15:23:11] mapped atoms in the reactants were not mapped in the products. +97: unmapped numbers are: 4 +97: [15:23:11] product atom-mapping number 5 not found in reactants. +98: ..[15:23:11] == testRGroupState +100: 1 smi: CC +100: 1 smi: CC +100: 2 smi: CCO[C@H](N)P +100: 2 smi: CC +89: [15:23:11] Explicit valence for atom # 27 P, 6, is greater than permitted +100: replaceSub smi1:CCP(CC)[C@@H](N)O +100: replaceSub smi1:CCNCC +98: .[15:23:11] == testRandomEnumerateAllBBsLibrary +98: ** [1, 1] +98: ** [0, 2] +98: ** [1, 0] +100: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O +100: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O +97: ........./build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +97: png = open(fname, 'rb').read() +97: ResourceWarning: Enable tracemalloc to get the object allocation traceback +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 34 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 36 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 38 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 40 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 42 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 87 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 89 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 91 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 93 +97: [15:23:11] Found a SCD/SED line with missing/empty SDT specification at line 95 +98: .[15:23:11] == testRandomEnumerateLibrary +98: .[15:23:11] == testRandomSample +98: .[15:23:11] == testRandomSampleAllBBs +100: [15:23:11] SMARTS Parse Error: syntax error while parsing: bar +100: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +97: ..[15:23:11] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [15:23:11] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [15:23:11] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [15:23:11] reaction has no reactants +97: [15:23:11] reaction has no products +97: [15:23:11] initialization failed +97: [15:23:11] reaction has no reactants +97: [15:23:11] reaction has no products + 89/235 Test #99: pyChemReactionSanitize ................. Passed 0.86 sec +test 101 + Start 101: chemTransformsTestCatch + +101: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms +101: Test timeout computed to be: 1500 +98: .[15:23:11] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: [15:23:11] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +98: .[15:23:11] == testRemoveBadMatches +98: .[15:23:11] == testTimings +97: .[15:23:11] SMARTS Parse Error: syntax error while parsing: boromicacid +97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +97: [15:23:11] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +97: [15:23:11] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +97: [15:23:11] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +97: [15:23:11] reaction has no reactants +97: [15:23:11] reaction has no products +97: [15:23:11] initialization failed +97: [15:23:11] reaction has no reactants +97: [15:23:11] reaction has no products +97: . +97: ---------------------------------------------------------------------- +97: Ran 54 tests in 0.231s +97: +97: OK +97: ******************************************** +97: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +97: + 90/235 Test #100: testChemTransforms ..................... Passed 0.16 sec +test 102 + Start 102: tautomerQueryTestCatch + +102: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +102: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery +102: Test timeout computed to be: 1500 +89: =============================================================================== +89: All tests passed (21562 assertions in 3 test cases) +89: + 91/235 Test #89: multithreadedSupplierCatchTest ......... Passed 3.14 sec +test 103 + Start 103: pyTautomerQuery + +103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +103: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +103: Test timeout computed to be: 1500 +101: Randomness seeded to: 3917734909 +101: [15:23:12] Incomplete atom labelling, cannot make bond +101: [15:23:12] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +101: [15:23:12] Incomplete atom labelling, cannot make bond +101: [15:23:12] +101: +101: **** +101: Invariant Violation +101: molzip: bond info already exists for end atom with label:1 +101: Violation occurred on line 992 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +101: Failed Expression: !bond.b +101: ---------- +101: Stacktrace: +101: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 +101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: ---------- +101: **** +101: +101: [15:23:12] Incomplete atom labelling, cannot make bond +101: [15:23:12] 101: 101: **** 101: Invariant Violation @@ -23827,24 +23884,30 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAABE9E6F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAABEA350AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAABEA35A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAABEA35E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAABEA0A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAABEA0A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAABE9DC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFFA22D229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAABE9DC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -89: [05:51:10] Explicit valence for atom # 10 Si, 6, is greater than permitted -101: [05:51:10] Incomplete atom labelling, cannot make bond -101: [05:51:10] Incomplete atom labelling, cannot make bond -101: [05:51:10] Incomplete atom labelling, cannot make bond -101: [05:51:10] + 92/235 Test #97: pyChemReactions ........................ Passed 1.27 sec +test 104 + Start 104: testSubgraphs1 + +104: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +104: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs +104: Test timeout computed to be: 1500 +101: [15:23:12] Incomplete atom labelling, cannot make bond +101: [15:23:12] Incomplete atom labelling, cannot make bond +101: [15:23:12] Incomplete atom labelling, cannot make bond +101: [15:23:12] 101: 101: **** 101: Invariant Violation @@ -23857,21 +23920,21 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAABE9E6F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAABEA350AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAABEA35A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAABEA35E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAABEA0A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAABEA0A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAABE9DC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFFA22D229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAABE9DC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [05:51:10] Incomplete atom labelling, cannot make bond -101: [05:51:10] +101: [15:23:12] Incomplete atom labelling, cannot make bond +101: [15:23:12] 101: 101: **** 101: Invariant Violation @@ -23884,20 +23947,22 @@ 101: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 4# 0x0000AAAABE9E6F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 5# 0x0000AAAABEA350AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAABEA35A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAABEA35E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAABEA0A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAABEA0A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAABE9DC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000FFFFA22D229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 4# 0x0000AAAAB8F06F60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 5# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 12# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 13# 0x0000AAAABE9DC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 13# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: -101: [05:51:10] +104: ----------------------- +104: Subgraph retrieval +101: [15:23:12] 101: 101: **** 101: Invariant Violation @@ -23911,66 +23976,55 @@ 101: 2# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&, std::optional, std::allocator > > >&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 3# RDKit::molzip(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 101: 4# RDKit::molzip(RDKit::ROMol const&, RDKit::MolzipParams const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitChemTransforms.so.1 -101: 5# 0x0000AAAABE9DD298 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 6# 0x0000AAAABEA350AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 7# 0x0000AAAABEA35A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 8# 0x0000AAAABEA35E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 9# 0x0000AAAABEA0A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 10# 0x0000AAAABEA0A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 11# 0x0000AAAABE9DC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -101: 12# 0x0000FFFFA22D229C in /lib/aarch64-linux-gnu/libc.so.6 +101: 5# 0x0000AAAAB8EFD298 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 6# 0x0000AAAAB8F550AC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 7# 0x0000AAAAB8F55A60 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 8# 0x0000AAAAB8F55E94 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 9# 0x0000AAAAB8F2A418 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 10# 0x0000AAAAB8F2A964 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 11# 0x0000AAAAB8EFC4D0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 12# 0x0000FFFFAB2B229C in /lib/aarch64-linux-gnu/libc.so.6 101: 13# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -101: 14# 0x0000AAAABE9DC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +101: 14# 0x0000AAAAB8EFC5B0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 101: ---------- 101: **** 101: 101: =============================================================================== 101: All tests passed (674 assertions in 9 test cases) 101: - 91/235 Test #101: chemTransformsTestCatch ................ Passed 0.16 sec -test 103 - Start 103: pyTautomerQuery - -103: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -103: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -103: Test timeout computed to be: 1500 -102: Randomness seeded to: 3771585624 -102: =============================================================================== -102: All tests passed (93 assertions in 13 test cases) -102: - 92/235 Test #102: tautomerQueryTestCatch ................. Passed 0.23 sec -test 104 - Start 104: testSubgraphs1 - -104: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -104: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs -104: Test timeout computed to be: 1500 - 93/235 Test #99: pyChemReactionSanitize ................. Passed 0.71 sec + 93/235 Test #101: chemTransformsTestCatch ................ Passed 0.22 sec test 105 Start 105: testSubgraphs2 105: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 105: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 105: Test timeout computed to be: 1500 -104: ----------------------- -104: Subgraph retrieval 104: Finished 104: ----------------------- 104: testSubgraphs2a 104: Finished 104: ----------------------- 104: testSubgraphs2 -89: [05:51:10] Explicit valence for atom # 2 O, 4, is greater than permitted 105: ----------------------- 105: Test1: pathToSubmol -89: [05:51:10] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [05:51:10] Explicit valence for atom # 3 Be, 4, is greater than permitted 105: Finished +104: Finished +104: ----------------------- +104: Path retrieval 105: ----------------------- 105: Test2: Atom Environments 105: Finished 105: ----------------------- 105: Test 3: Atom Environments (Extension) +104: Finished +104: ----------------------- +104: Path retrieval2 +104: Finished +104: ----------------------- +104: Unique Subgraph retrieval +104: Finished +104: ----------------------- +104: testUniqueSubgraphs2 105: Finished 105: ----------------------- 105: Testing github Issue103: stereochemistry and pathToSubmol @@ -23978,57 +24032,29 @@ 105: ----------------------- 105: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 105: Finished - 94/235 Test #105: testSubgraphs2 ......................... Passed 0.07 sec + 94/235 Test #105: testSubgraphs2 ......................... Passed 0.10 sec test 106 Start 106: subgraphsCatch 106: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 106: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 106: Test timeout computed to be: 1500 -89: [05:51:10] Explicit valence for atom # 27 P, 6, is greater than permitted -106: Randomness seeded to: 860974484 -106: --------- -106: =============================================================================== -106: All tests passed (11 assertions in 1 test case) -106: - 95/235 Test #106: subgraphsCatch ......................... Passed 0.04 sec +102: Randomness seeded to: 2267052945 +102: =============================================================================== +102: All tests passed (93 assertions in 13 test cases) +102: + 95/235 Test #102: tautomerQueryTestCatch ................. Passed 0.35 sec test 107 Start 107: filterCatalogTest 107: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 107: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog 107: Test timeout computed to be: 1500 -104: Finished -29: All 191 tests passed -104: ----------------------- -104: Path retrieval -104: Finished -104: ----------------------- -104: Path retrieval2 -104: Finished -104: ----------------------- -104: Unique Subgraph retrieval -104: Finished -104: ----------------------- -104: testUniqueSubgraphs2 -98: . -98: ---------------------------------------------------------------------- -98: Ran 11 tests in 0.882s -98: -98: OK -98: True -98: == CartesianProductStrategy CartesianProductStrategy -98: 197 out of 300 -98: 0 6 out of 10 -98: 1 3 out of 5 -98: 2 4 out of 6 -98: 198 out of 300 -98: 0 10 out of 10 -98: 1 5 out of 5 -98: 2 6 out of 6 -98: Skipped 10000000 in 0.06286001205444336 seconds -98: Skipped 10000000 in 0.4324498176574707 seconds -98: Skipped 10000000 in 0.08013701438903809 seconds +103: ..... +103: ---------------------------------------------------------------------- +103: Ran 5 tests in 0.053s +103: +103: OK 107: Warning: molecule failed filter 107: Warning: molecule failed filter: reason hzone_phenol_A(479) 107: v = { @@ -24088,13 +24114,6 @@ 107: 12,16}, 107: } 107: Warning: molecule failed filter - 96/235 Test #98: pyChemReactionEnumerations ............. Passed 1.32 sec -test 108 - Start 108: pyFilterCatalog - -108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -108: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -108: Test timeout computed to be: 1500 107: Warning: molecule failed filter: reason keto_keto_gamma(5) 107: v = { 107: 0,0}, @@ -24124,21 +24143,6 @@ 107: 10,15}, 107: 11,16}, 107: } -103: ..... -103: ---------------------------------------------------------------------- -103: Ran 5 tests in 0.045s -103: -103: OK -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... - 97/235 Test #103: pyTautomerQuery ........................ Passed 0.55 sec -test 109 - Start 109: testFragCatalog - -109: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog -109: Test timeout computed to be: 1500 -109: 21 104: Finished 104: ----------------------- 104: testRootedSubgraphs @@ -24146,99 +24150,117 @@ 104: ----------------------- 104: testRootedPaths 104: Finished - 98/235 Test #104: testSubgraphs1 ......................... Passed 0.59 sec + 96/235 Test #104: testSubgraphs1 ......................... Passed 0.40 sec +test 108 + Start 108: pyFilterCatalog + +108: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +108: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +108: Test timeout computed to be: 1500 +106: Randomness seeded to: 4069095747 +106: --------- + 97/235 Test #103: pyTautomerQuery ........................ Passed 0.51 sec +test 109 + Start 109: testFragCatalog + +109: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog +109: Test timeout computed to be: 1500 +106: =============================================================================== +106: All tests passed (11 assertions in 1 test case) +106: + 98/235 Test #106: subgraphsCatch ......................... Passed 0.30 sec test 110 Start 110: pyFragCatalog 110: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 110: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 110: Test timeout computed to be: 1500 - 99/235 Test #107: filterCatalogTest ...................... Passed 0.52 sec +109: 21 + 99/235 Test #107: filterCatalogTest ...................... Passed 0.35 sec test 111 Start 111: testDescriptors 111: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 111: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test Crippen parameter acquisition. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test Crippen calculation. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test Issue262: problems with Crippen calculation from pickles. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test AMW calculation. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test Exact MW calculation. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test Labute ASA descriptors. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test TPSA descriptors. -89: [05:51:11] Explicit valence for atom # 9 N, 6, is greater than permitted +111: [15:23:12] ------------------------------------- +111: [15:23:12] Test Crippen parameter acquisition. +111: [15:23:12] done +111: [15:23:12] ------------------------------------- +111: [15:23:12] Test Crippen calculation. +111: [15:23:12] done +111: [15:23:12] ------------------------------------- +111: [15:23:12] Test Issue262: problems with Crippen calculation from pickles. +111: [15:23:12] done +111: [15:23:12] ------------------------------------- +111: [15:23:12] Test AMW calculation. +111: [15:23:12] done +111: [15:23:12] ------------------------------------- +111: [15:23:12] Test Exact MW calculation. +111: [15:23:12] done +111: [15:23:12] ------------------------------------- +111: [15:23:12] Test Labute ASA descriptors. +111: [15:23:12] done +111: [15:23:12] ------------------------------------- +111: [15:23:12] Test TPSA descriptors. +111: [15:23:12] done +111: [15:23:12] ------------------------------------- +111: [15:23:12] Test Lipinski parameters. 108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. 108: :488: RuntimeWarning: to-Python converter for boost::shared_ptr already registered; second conversion method ignored. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test Lipinski parameters. -89: [05:51:11] Explicit valence for atom # 3 Al, 6, is greater than permitted +98: . +98: ---------------------------------------------------------------------- +98: Ran 11 tests in 1.294s +98: +98: OK +98: True +98: == CartesianProductStrategy CartesianProductStrategy +98: 197 out of 300 +98: 0 6 out of 10 +98: 1 3 out of 5 +98: 2 4 out of 6 +98: 198 out of 300 +98: 0 10 out of 10 +98: 1 5 out of 5 +98: 2 6 out of 6 +98: Skipped 10000000 in 0.07905292510986328 seconds +98: Skipped 10000000 in 0.6406230926513672 seconds +98: Skipped 10000000 in 0.16956377029418945 seconds +111: [15:23:13] done +111: [15:23:13] ------------------------------------- +111: [15:23:13] Test VSA descriptors. +111: [15:23:13] done +111: [15:23:13] ------------------------------------- +111: [15:23:13] Test molecular formula calculation. +111: [15:23:13] done +111: [15:23:13] ------------------------------------- +111: [15:23:13] Test Issue 3415534. +111: [15:23:13] done +111: [15:23:13] ------------------------------------- +111: [15:23:13] Test Issue3433771: Bad definition for Crippen atom type O11. +111: [15:23:13] done +111: [15:23:13] ------------------------------------- +111: [15:23:13] Test multithreading +111: reading molecules 110: ......... 110: ---------------------------------------------------------------------- -110: Ran 9 tests in 0.055s +110: Ran 9 tests in 0.092s 110: 110: OK -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test VSA descriptors. -89: [05:51:11] Explicit valence for atom # 4 Al, 6, is greater than permitted -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test molecular formula calculation. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test Issue 3415534. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test Issue3433771: Bad definition for Crippen atom type O11. -111: [05:51:11] done -111: [05:51:11] ------------------------------------- -111: [05:51:11] Test multithreading -111: reading molecules -89: [05:51:11] Explicit valence for atom # 10 Si, 6, is greater than permitted 111: processing 111: launch :0 111: launch :1 111: launch :2 111: launch :3 -100/235 Test #110: pyFragCatalog .......................... Passed 0.51 sec +100/235 Test #98: pyChemReactionEnumerations ............. Passed 2.29 sec test 112 Start 112: testAUTOCORR2D 112: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 112: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -112: [05:51:11] ---------------------------- -112: start test autocorr2D -89: [05:51:11] Explicit valence for atom # 2 O, 4, is greater than permitted -89: [05:51:11] Explicit valence for atom # 3 Al, 6, is greater than permitted -89: [05:51:11] Explicit valence for atom # 3 Be, 4, is greater than permitted -89: [05:51:11] Explicit valence for atom # 27 P, 6, is greater than permitted -89: =============================================================================== -89: All tests passed (21562 assertions in 3 test cases) -89: -101/235 Test #89: multithreadedSupplierCatchTest ......... Passed 3.94 sec -test 113 - Start 113: testATF - -113: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF -113: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -113: Test timeout computed to be: 1500 -109: [05:51:11] +109: [15:23:13] 109: 109: **** 109: Invariant Violation @@ -24249,17 +24271,17 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFBC671948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFB24C1948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAC08B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAC08B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBBC4229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAADA5B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAADA5B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFB1A9229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAC08B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAADA5B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [05:51:11] +109: [15:23:13] 109: 109: **** 109: Invariant Violation @@ -24270,17 +24292,17 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFBC671948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFB24C1948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAC08B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAC08B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBBC4229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAADA5B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAADA5B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFB1A9229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAC08B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAADA5B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -109: [05:51:11] +109: [15:23:13] 109: 109: **** 109: Invariant Violation @@ -24291,774 +24313,614 @@ 109: Stacktrace: 109: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 109: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -109: 2# 0x0000FFFFBC671948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 +109: 2# 0x0000FFFFB24C1948 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 109: 3# RDKit::readFuncGroups(std::istream&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitFragCatalog.so.1 -109: 4# 0x0000AAAAC08B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 5# 0x0000AAAAC08B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -109: 6# 0x0000FFFFBBC4229C in /lib/aarch64-linux-gnu/libc.so.6 +109: 4# 0x0000AAAADA5B7ADC in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 5# 0x0000AAAADA5B49E0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 6# 0x0000FFFFB1A9229C in /lib/aarch64-linux-gnu/libc.so.6 109: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -109: 8# 0x0000AAAAC08B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +109: 8# 0x0000AAAADA5B4BB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 109: ---------- 109: **** 109: -102/235 Test #109: testFragCatalog ........................ Passed 0.93 sec +101/235 Test #109: testFragCatalog ........................ Passed 0.63 sec +test 113 + Start 113: testATF + +113: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF +113: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +113: Test timeout computed to be: 1500 +112: [15:23:13] ---------------------------- +112: start test autocorr2D +102/235 Test #113: testATF ................................ Passed 0.04 sec test 114 Start 114: testBCUT 114: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 114: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 114: Test timeout computed to be: 1500 -103/235 Test #113: testATF ................................ Passed 0.04 sec +103/235 Test #110: pyFragCatalog .......................... Passed 0.66 sec test 115 Start 115: testEEM 115: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM 115: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 115: Test timeout computed to be: 1500 -114: [05:51:11] ------------------------------------- -114: [05:51:11] Basic BCUT tests. -114: [05:51:11] done -114: [05:51:11] ------------------------------------- -114: [05:51:11] Larger BCUT tests. +114: [15:23:13] ------------------------------------- +114: [15:23:13] Basic BCUT tests. +114: [15:23:13] done +114: [15:23:13] ------------------------------------- +114: [15:23:13] Larger BCUT tests. 115: =>start test EEM -115: [05:51:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 115: 0 -115: [05:51:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -112: [05:51:12] done -112: [05:51:12] ------------------------------------- -112: [05:51:12] Test Github #3806: NaNs from AUTOCORR2D descriptor -112: [05:51:12] done -104/235 Test #112: testAUTOCORR2D ......................... Passed 0.41 sec +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 100 +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 200 +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .............[15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +108: [15:23:13] SMILES Parse Error: syntax error while parsing: --- +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] --- +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +108: [15:23:13] dasfsadf +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: .[15:23:13] SMILES Parse Error: syntax error while parsing: mydoghasfleas +108: [15:23:13] SMILES Parse Error: check for mistakes around position 1: +108: [15:23:13] mydoghasfleas +108: [15:23:13] ^ +108: [15:23:13] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +29: All 191 tests passed +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 300 +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +112: [15:23:13] done +112: [15:23:13] ------------------------------------- +112: [15:23:13] Test Github #3806: NaNs from AUTOCORR2D descriptor +112: [15:23:13] done +104/235 Test #112: testAUTOCORR2D ......................... Passed 0.74 sec test 116 Start 116: testPBF 116: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF 116: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 116: Test timeout computed to be: 1500 -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [05:51:12] ------------------------------------- -116: [05:51:12] Basic PBF tests. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 100 -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 200 -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -116: [05:51:12] done -116: [05:51:12] ------------------------------------- -116: [05:51:12] PBF edge cases. -116: [05:51:12] done -105/235 Test #116: testPBF ................................ Passed 0.23 sec -test 117 - Start 117: testRDFcustom - -117: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -117: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -117: Test timeout computed to be: 1500 -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 300 -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: 400 -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: [05:51:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -115: Elapsed time: 0.714639 s -115: Errors:0 -115: [05:51:12] test on : 500 molecules done -106/235 Test #115: testEEM ................................ Passed 0.74 sec -test 118 - Start 118: testRDF - -118: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF -118: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -118: Test timeout computed to be: 1500 -108: .............[05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -108: [05:51:12] SMILES Parse Error: syntax error while parsing: --- -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] --- -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -108: [05:51:12] dasfsadf -114: [05:51:12] ------------------------------------- -114: [05:51:12] Test empty molecule BCUT. -107/235 Test #114: testBCUT ............................... Passed 0.86 sec -test 119 - Start 119: testMORSE - -119: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE -119: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -119: Test timeout computed to be: 1500 -108: .[05:51:12] SMILES Parse Error: syntax error while parsing: mydoghasfleas -108: [05:51:12] SMILES Parse Error: check for mistakes around position 1: -108: [05:51:12] mydoghasfleas -108: [05:51:12] ^ -108: [05:51:12] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -117: =>start test rdf custom -117: [05:51:12] test on : 365 molecules done +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +75: [15:23:13] Finished: testSmiCorrectness() +75: [15:23:13] ----------------------------------------- +75: +75: [15:23:13] +75: ----------------------------------------- +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [15:23:13] ------------------------------------- +116: [15:23:13] Basic PBF tests. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +75: [15:23:13] Spurious data before the first property will be ignored +75: [15:23:13] Property will be truncated after the first blank line +75: [15:23:13] Property will be truncated after the first blank line +75: [15:23:13] Property will be truncated after the first blank line +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 108: ....... 108: ---------------------------------------------------------------------- -108: Ran 21 tests in 1.768s +108: Ran 21 tests in 1.069s 108: 108: OK 108: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -25080,201 +24942,366 @@ 108: 1 108: 2 108: running -75: [05:51:13] Finished: testSmiCorrectness() -75: [05:51:13] ----------------------------------------- -75: -75: [05:51:13] -75: ----------------------------------------- -108/235 Test #108: pyFilterCatalog ........................ Passed 2.44 sec +115: [15:23:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105/235 Test #108: pyFilterCatalog ........................ Passed 1.54 sec +test 117 + Start 117: testRDFcustom + +117: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +117: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +117: Test timeout computed to be: 1500 +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: [15:23:14] ------------------------------------- +114: [15:23:14] Test empty molecule BCUT. +106/235 Test #114: testBCUT ............................... Passed 0.87 sec +test 118 + Start 118: testRDF + +118: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF +118: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +118: Test timeout computed to be: 1500 +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: 400 +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [15:23:14] done +116: [15:23:14] ------------------------------------- +116: [15:23:14] PBF edge cases. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [15:23:14] done +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +107/235 Test #116: testPBF ................................ Passed 0.27 sec +test 119 + Start 119: testMORSE + +119: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE +119: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +119: Test timeout computed to be: 1500 +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: [15:23:14] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +115: Elapsed time: 0.994021 s +115: Errors:0 +115: [15:23:14] test on : 500 molecules done +108/235 Test #115: testEEM ................................ Passed 1.05 sec test 120 Start 120: test3D 120: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 120: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 120: Test timeout computed to be: 1500 -120: [05:51:13] ------------------------------------- -120: [05:51:13] Basic PMI tests. -75: [05:51:13] Property will be truncated after the first blank line -75: [05:51:13] Property will be truncated after the first blank line -75: [05:51:13] Spurious data before the first property will be ignored -75: [05:51:13] Property will be truncated after the first blank line +120: [15:23:14] ------------------------------------- +120: [15:23:14] Basic PMI tests. +120: [15:23:14] done +120: [15:23:14] ------------------------------------- +120: [15:23:14] More PMI/NPR tests. +120: [15:23:14] done +120: [15:23:14] ------------------------------------- +120: [15:23:14] Basic NPR tests. +117: =>start test rdf custom +117: [15:23:14] test on : 365 molecules done 118: =>start test rdf -118: [05:51:13] test on : 365 molecules done -109/235 Test #118: testRDF ................................ Passed 0.73 sec +118: [15:23:14] test on : 365 molecules done +109/235 Test #118: testRDF ................................ Passed 0.66 sec test 121 Start 121: testWHIM 121: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 121: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 121: Test timeout computed to be: 1500 -120: [05:51:13] done -120: [05:51:13] ------------------------------------- -120: [05:51:13] More PMI/NPR tests. -120: [05:51:13] done -120: [05:51:13] ------------------------------------- -120: [05:51:13] Basic NPR tests. -29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -29: All 191 tests passed -120: [05:51:13] done -120: [05:51:13] ------------------------------------- -120: [05:51:13] PMI edge cases. -120: [05:51:13] done -120: [05:51:13] ------------------------------------- -120: [05:51:13] NPR edge cases. -120: [05:51:13] done -120: [05:51:13] ------------------------------------- -120: [05:51:13] 3D descriptors. -120: [05:51:13] done -120: [05:51:13] ------------------------------------- -120: [05:51:13] 3D descriptor edge cases. -120: [05:51:13] done -120: [05:51:13] ------------------------------------- -120: [05:51:13] Inertial shape factor. -120: [05:51:13] done -110/235 Test #120: test3D ................................. Passed 0.52 sec +120: [15:23:14] done +120: [15:23:14] ------------------------------------- +120: [15:23:14] PMI edge cases. +120: [15:23:14] done +120: [15:23:14] ------------------------------------- +120: [15:23:14] NPR edge cases. +120: [15:23:14] done +120: [15:23:14] ------------------------------------- +120: [15:23:14] 3D descriptors. +120: [15:23:14] done +120: [15:23:14] ------------------------------------- +120: [15:23:14] 3D descriptor edge cases. +120: [15:23:14] done +120: [15:23:14] ------------------------------------- +120: [15:23:14] Inertial shape factor. +120: [15:23:14] done +110/235 Test #120: test3D ................................. Passed 0.47 sec test 122 Start 122: testGETAWAY 122: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 122: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 122: Test timeout computed to be: 1500 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -119: =>start test MORSE -119: =>read file -119: [05:51:13] test on : 365 molecules done -111/235 Test #119: testMORSE .............................. Passed 1.07 sec +75: [15:23:14] Finished: testSDCorrectness() +75: [15:23:14] ----------------------------------------- +75: +111/235 Test #75: testMultithreadedMolSupplier ........... Passed 7.06 sec test 123 Start 123: testAUTOCORR3D 123: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 123: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 123: Test timeout computed to be: 1500 -121: =>start test WHIM -121: [05:51:13] test on : 365 molecules done -112/235 Test #121: testWHIM ............................... Passed 0.50 sec +119: =>start test MORSE +119: =>read file +119: [15:23:15] test on : 365 molecules done +112/235 Test #119: testMORSE .............................. Passed 0.94 sec test 124 Start 124: testCoulombMat 124: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 124: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 124: Test timeout computed to be: 1500 -117: =>start test morse custom -117: [05:51:13] test on : 365 molecules done 124: ===================== Testing CoulombMat ======================= -124: CM test 1 mat Done -113/235 Test #124: testCoulombMat ......................... Passed 0.06 sec +121: =>start test WHIM +121: [15:23:15] test on : 365 molecules done +113/235 Test #121: testWHIM ............................... Passed 0.41 sec test 125 Start 125: descriptorsTestCatch 125: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 125: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 125: Test timeout computed to be: 1500 -125: Randomness seeded to: 2354657248 -125: Warning: Atom Count for residue GLU5A does not match expected count -125: Warning: Atom Count for residue ASN39A does not match expected count -125: Warning: Atom Count for residue GLU53A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count -125: Warning: Atom Count for residue LYS80A does not match expected count -125: Warning: Atom Count for residue GLU150A does not match expected count -125: Warning: Atom Count for residue ASN157A does not match expected count -75: [05:51:14] Finished: testSDCorrectness() -75: [05:51:14] ----------------------------------------- -75: -114/235 Test #75: testMultithreadedMolSupplier ........... Passed 7.05 sec +124: CM test 1 mat Done +114/235 Test #124: testCoulombMat ......................... Passed 0.06 sec test 126 Start 126: pyMolDescriptors 126: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 126: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 126: Test timeout computed to be: 1500 +125: Randomness seeded to: 3339088346 125: Warning: Atom Count for residue GLU5A does not match expected count +125: Warning: Atom Count for residue ASN39A does not match expected count +125: Warning: Atom Count for residue GLU53A does not match expected count +125: Warning: Atom Count for residue ARG64A does not match expected count +125: Warning: Atom Count for residue LYS80A does not match expected count +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test Issue252: Bad definitions for Crippen atom types. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test calculation of ChiVs. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test calculation of ChiNs. +125: Warning: Atom Count for residue GLU150A does not match expected count +125: Warning: Atom Count for residue ASN157A does not match expected count +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test calculation of HallKierAlpha. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test calculation of Kappa1. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test calculation of Kappa2. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test calculation of Kappa3. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test Crippen atom type calculations. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test ring descriptors +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test other count descriptors. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test MQN +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test GitHub Issue 56. +111: [15:23:15] WARNING: not removing hydrogen atom without neighbors +111: [15:23:15] WARNING: not removing hydrogen atom without neighbors +111: [15:23:15] WARNING: not removing hydrogen atom without neighbors +111: [15:23:15] WARNING: not removing hydrogen atom without neighbors +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test Github92: Bad Crippen atom type for pyrrole H. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test Github362: order dependence in Kier-Hall descriptors. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test calculation of spiro and bridgehead counts. +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test Github694: ExactMolWt ignoring the mass of the electron +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Testing Properties and KitchenSink +111: [15:23:15] ---Caught keyerror (bad property name)--- +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test USR Descriptor +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test Github #1973: support P and S terms for TPSA calculation +111: [15:23:15] done +111: [15:23:15] ------------------------------------- +111: [15:23:15] Test Github #2948: Empty molecule has non-zero LabuteASA +111: [15:23:15] done 123: =>start test autocorr3D -123: [05:51:14] test on : 365 molecules done -115/235 Test #123: testAUTOCORR3D ......................... Passed 0.52 sec +123: [15:23:15] test on : 365 molecules done +115/235 Test #111: testDescriptors ........................ Passed 2.66 sec +116/235 Test #123: testAUTOCORR3D ......................... Passed 0.43 sec test 127 Start 127: pyMolDescriptors3D 127: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Descriptors/Wrap/test3D.py" 127: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 127: Test timeout computed to be: 1500 -117: =>start test AUTOCORR3D custom -117: [05:51:14] test on : 365 molecules done -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test Issue252: Bad definitions for Crippen atom types. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test calculation of ChiVs. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test calculation of ChiNs. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test calculation of HallKierAlpha. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test calculation of Kappa1. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test calculation of Kappa2. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test calculation of Kappa3. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test Crippen atom type calculations. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test ring descriptors -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test other count descriptors. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test MQN -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test GitHub Issue 56. -111: [05:51:14] WARNING: not removing hydrogen atom without neighbors -111: [05:51:14] WARNING: not removing hydrogen atom without neighbors -111: [05:51:14] WARNING: not removing hydrogen atom without neighbors -111: [05:51:14] WARNING: not removing hydrogen atom without neighbors -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test Github92: Bad Crippen atom type for pyrrole H. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test Github362: order dependence in Kier-Hall descriptors. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test calculation of spiro and bridgehead counts. -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test Github694: ExactMolWt ignoring the mass of the electron -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Testing Properties and KitchenSink -111: [05:51:14] ---Caught keyerror (bad property name)--- -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test USR Descriptor -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test Github #1973: support P and S terms for TPSA calculation -111: [05:51:14] done -111: [05:51:14] ------------------------------------- -111: [05:51:14] Test Github #2948: Empty molecule has non-zero LabuteASA -111: [05:51:14] done -116/235 Test #111: testDescriptors ........................ Passed 3.32 sec test 128 Start 128: testFingerprints 128: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 128: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 128: Test timeout computed to be: 1500 +125: Warning: Atom Count for residue GLU5A does not match expected count 128: 128: 128: @@ -25758,427 +25785,194 @@ 128: 128: ------------------- 128: -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Morgan Fingerprints. -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Morgan Fingerprints using fromAtoms argument. -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Morgan Fingerprints as bit vects. -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Morgan Fingerprints with feature invariants. -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test additional Morgan fingerprints options. -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Atom Codes. -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Atom Pairs. -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Atom Pairs part 2. -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Topological Torsions. -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Bulk Topological Torsions. -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -117: =>start test 2 WHIM custom -117: [05:51:14] test on : 365 molecules done -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Hashed Atom Pairs. -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Hashed torsions. -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Rooted Atom Pairs. -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test ignoring atoms in Atom Pairs. -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Rooted Topological Torsions. -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test ignoring atoms in Topological Torsions. -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test atom info from morgan fingerprints. -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test atom info from morgan fingerprints including Info Redundant Environments. -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] ------------------------------------- -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] ------------------------------------- -128: [05:51:14] ------------------------------------- -128: [05:51:14] ------------------------------------- -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Atom Pairs including info about chirality. -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test Topological Torsions including info about chirality. -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test GitHub Issue 25: fingerprint backwards compatibility. -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test GitHub Issue 151: PatternFingerprint problems -125: Warning: Atom Count for residue ASN39A does not match expected count -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test 3D atom pairs. -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -128: [05:51:14] done -128: [05:51:14] ------------------------------------- -128: [05:51:14] Test multithreading with the pattern FP -128: reading molecules -128: pass 1 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -117: =>start test 1 WHIM custom -117: [05:51:14] test on : 365 molecules done -125: Warning: Atom Count for residue GLU53A does not match expected count -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:14] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: .[05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:14] DEPRECATION WARNING: please use AtomPairGenerator -128: pass 2 -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -126: ..[05:51:14] +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Morgan Fingerprints. +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Morgan Fingerprints using fromAtoms argument. +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Morgan Fingerprints as bit vects. +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Morgan Fingerprints with feature invariants. +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test additional Morgan fingerprints options. +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Atom Codes. +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Atom Pairs. +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Atom Pairs part 2. +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Topological Torsions. +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Bulk Topological Torsions. +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: .[15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[15:23:15] 126: 126: **** +125: Warning: Atom Count for residue ASN39A does not match expected count +117: =>start test morse custom +117: [15:23:15] test on : 365 molecules done 126: Pre-condition Violation 126: Number of atom props not equal to number of atoms 126: Violation occurred on line 89 in file ./Code/GraphMol/Descriptors/BCUT.cpp @@ -26188,10 +25982,10 @@ 126: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 126: 2# RDKit::Descriptors::BCUT2D(RDKit::ROMol const&, std::vector > const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitDescriptors.so.1 -126: 3# 0x0000FFFF9D6BD098 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so -126: 4# 0x0000FFFF9D6D1350 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 3# 0x0000FFFF85E5D098 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so +126: 4# 0x0000FFFF85E71350 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdMolDescriptors.so 126: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 6# 0x0000FFFFA1532680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 6# 0x0000FFFF89CD2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 126: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -26202,17 +25996,17 @@ 126: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 126: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 126: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 17# 0x0000FFFF9FB0B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 18# 0x0000FFFF9FB0B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 19# 0x0000FFFF9FB0B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 20# 0x0000FFFF9FB0B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -126: 21# 0x0000FFFF9FB0B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 17# 0x0000FFFF882AB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 18# 0x0000FFFF882AB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 19# 0x0000FFFF882AB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 20# 0x0000FFFF882AB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +126: 21# 0x0000FFFF882AB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 126: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 126: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 126: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 126: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 126: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -126: 27# 0x0000FFFFA152F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +126: 27# 0x0000FFFF89CCF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 126: 28# _PyObject_MakeTpCall in /usr/bin/python3 126: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 126: 30# 0x00000000005335D0 in /usr/bin/python3 @@ -26244,223 +26038,462 @@ 126: 56# 0x0000000000627010 in /usr/bin/python3 126: 57# Py_RunMain in /usr/bin/python3 126: 58# Py_BytesMain in /usr/bin/python3 -126: 59# 0x0000FFFFA1E3229C in /lib/aarch64-linux-gnu/libc.so.6 +126: 59# 0x0000FFFF8A5D229C in /lib/aarch64-linux-gnu/libc.so.6 126: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 126: 61# _start in /usr/bin/python3 126: ---------- 126: **** 126: +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ...Warning: Atom Count for residue GLU5A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: Warning: Atom Count for residue ARG64A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count -125: Warning: Atom Count for residue ARG64A does not match expected count +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Hashed Atom Pairs. +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Hashed torsions. +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Rooted Atom Pairs. +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test ignoring atoms in Atom Pairs. +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Rooted Topological Torsions. +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test ignoring atoms in Topological Torsions. +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test atom info from morgan fingerprints. +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test atom info from morgan fingerprints including Info Redundant Environments. +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] ------------------------------------- +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] ------------------------------------- +125: Warning: Atom Count for residue GLU53A does not match expected count +128: [15:23:15] ------------------------------------- +128: [15:23:15] ------------------------------------- +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Atom Pairs including info about chirality. +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test Topological Torsions including info about chirality. +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test GitHub Issue 25: fingerprint backwards compatibility. +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test GitHub Issue 151: PatternFingerprint problems +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test 3D atom pairs. +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +128: [15:23:15] done +128: [15:23:15] ------------------------------------- +128: [15:23:15] Test multithreading with the pattern FP +128: reading molecules 126: Warning: Atom Count for residue GLU5A does not match expected count +125: Warning: Atom Count for residue ARG64A does not match expected count +128: pass 1 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +125: Warning: Atom Count for residue LYS80A does not match expected count +128: pass 2 +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +117: =>start test AUTOCORR3D custom +117: [15:23:15] test on : 365 molecules done 127: ........ 127: ---------------------------------------------------------------------- -127: Ran 8 tests in 0.270s +127: Ran 8 tests in 0.233s 127: 127: OK -125: Warning: Atom Count for residue LYS80A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count -126: Warning: Atom Count for residue GLU53A does not match expected count -117/235 Test #127: pyMolDescriptors3D ..................... Passed 0.99 sec +117/235 Test #127: pyMolDescriptors3D ..................... Passed 0.87 sec test 129 Start 129: testMHFPFingerprint 129: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 129: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 129: Test timeout computed to be: 1500 -129: [05:51:15] ------------------------------------- -129: [05:51:15] Test MHFP fingerprint encoder initialization -129: [05:51:15] done -129: [05:51:15] ------------------------------------- -129: [05:51:15] Test MHFP shingling creation -129: [05:51:15] done -129: [05:51:15] ------------------------------------- -129: [05:51:15] Test MHFP hashing of string and uint arrays -129: [05:51:15] done -129: [05:51:15] ------------------------------------- -129: [05:51:15] Test SECFP fingerprint functionality -129: [05:51:15] done -118/235 Test #129: testMHFPFingerprint .................... Passed 0.08 sec +117: =>start test 2 WHIM custom +117: [15:23:16] test on : 365 molecules done +129: [15:23:16] ------------------------------------- +129: [15:23:16] Test MHFP fingerprint encoder initialization +129: [15:23:16] done +129: [15:23:16] ------------------------------------- +129: [15:23:16] Test MHFP shingling creation +126: Warning: Atom Count for residue GLU53A does not match expected count +129: [15:23:16] done +129: [15:23:16] ------------------------------------- +129: [15:23:16] Test MHFP hashing of string and uint arrays +129: [15:23:16] done +129: [15:23:16] ------------------------------------- +129: [15:23:16] Test SECFP fingerprint functionality +129: [15:23:16] done +118/235 Test #129: testMHFPFingerprint .................... Passed 0.12 sec test 130 Start 130: testFingerprintGenerators 130: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 130: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 130: Test timeout computed to be: 1500 +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test atom-pair fp generator +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test atom-pair fp generator with different arguments +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] DEPRECATION WARNING: please use AtomPairGenerator +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test atom-pair additional output +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Folded Atom Pairs. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Rooted Atom Pairs. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test ignoring atoms in Atom Pairs. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Atom Pairs including info about chirality. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Morgan Fingerprints. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test morgan fp generator +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Morgan Fingerprints using fromAtoms argument. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Morgan Fingerprints as bit vects. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Morgan Fingerprints with feature invariants. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test additional Morgan fingerprints options. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Single atoms setting radius 1 bits in Morgan fingerprints +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test different invariant generator combinations 126: Warning: Atom Count for residue ARG64A does not match expected count -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test atom-pair fp generator -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test atom-pair fp generator with different arguments -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] DEPRECATION WARNING: please use AtomPairGenerator -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test atom-pair additional output -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Folded Atom Pairs. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Rooted Atom Pairs. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test ignoring atoms in Atom Pairs. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Atom Pairs including info about chirality. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Morgan Fingerprints. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test morgan fp generator -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Morgan Fingerprints using fromAtoms argument. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Morgan Fingerprints as bit vects. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Morgan Fingerprints with feature invariants. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test additional Morgan fingerprints options. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Single atoms setting radius 1 bits in Morgan fingerprints -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test different invariant generator combinations -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test invariant overriding -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test RDKit fp generator +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test invariant overriding +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test RDKit fp generator +125: Warning: Atom Count for residue GLU150A does not match expected count +117: =>start test 1 WHIM custom +117: [15:23:16] test on : 365 molecules done +125: Warning: Atom Count for residue ASN157A does not match expected count 126: Warning: Atom Count for residue LYS80A does not match expected count -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test unfolded version of RDKFP -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test topological torsion fp generator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] DEPRECATION WARNING: please use TopologicalTorsionGenerator -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Topological Torsions. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Folded torsions. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Bulk Topological Torsions. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Rooted Topological Torsions. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test ignoring atoms in Topological Torsions. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test Topological Torsions including info about chirality. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test GitHub Issue 25: fingerprint backwards compatibility. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -130: [05:51:15] done -130: [05:51:15] ------------------------------------- -130: [05:51:15] Test convenience and bulk fp calculation functions +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test unfolded version of RDKFP +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test topological torsion fp generator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] DEPRECATION WARNING: please use TopologicalTorsionGenerator +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Topological Torsions. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Folded torsions. +130: [15:23:16] done +130: [15:23:16] ------------------------------------- +130: [15:23:16] Test Bulk Topological Torsions. 122: =>start test GETAWAY -122: [05:51:16] test on : 365 molecules done -119/235 Test #122: testGETAWAY ............................ Passed 2.36 sec +122: [15:23:17] test on : 365 molecules done +119/235 Test #122: testGETAWAY ............................ Passed 2.33 sec test 131 Start 131: fpTestCatch 131: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 131: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 131: Test timeout computed to be: 1500 -130: [05:51:16] done -130: [05:51:16] ------------------------------------- -130: [05:51:16] Test GitHub Issue #6958 -130: [05:51:16] DEPRECATION WARNING: please use AtomPairGenerator -120/235 Test #130: testFingerprintGenerators .............. Passed 0.74 sec +130: [15:23:17] done +130: [15:23:17] ------------------------------------- +130: [15:23:17] Test Rooted Topological Torsions. +130: [15:23:17] done +130: [15:23:17] ------------------------------------- +130: [15:23:17] Test ignoring atoms in Topological Torsions. +130: [15:23:17] done +130: [15:23:17] ------------------------------------- +130: [15:23:17] ------------------------------------- +130: [15:23:17] Test Topological Torsions including info about chirality. +130: [15:23:17] done +130: [15:23:17] ------------------------------------- +130: [15:23:17] Test GitHub Issue 25: fingerprint backwards compatibility. +130: [15:23:17] done +130: [15:23:17] ------------------------------------- +130: [15:23:17] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +130: [15:23:17] done +130: [15:23:17] ------------------------------------- +130: [15:23:17] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +130: [15:23:17] done +130: [15:23:17] ------------------------------------- +130: [15:23:17] Test convenience and bulk fp calculation functions +131: Randomness seeded to: 3867264887 +131: =============================================================================== +131: All tests passed (188 assertions in 16 test cases) +131: +120/235 Test #131: fpTestCatch ............................ Passed 0.09 sec test 132 Start 132: fpGenTestCatch 132: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 132: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 132: Test timeout computed to be: 1500 -131: Randomness seeded to: 4207841261 -131: =============================================================================== -131: All tests passed (188 assertions in 16 test cases) -131: -121/235 Test #131: fpTestCatch ............................ Passed 0.07 sec +132: Randomness seeded to: 3045650141 +132: =============================================================================== +132: All tests passed (2737 assertions in 7 test cases) +132: +121/235 Test #132: fpGenTestCatch ......................... Passed 0.22 sec test 133 Start 133: pyTestGenerator 133: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 133: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 133: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue GLU150A does not match expected count -132: Randomness seeded to: 2554223453 -132: =============================================================================== -132: All tests passed (2737 assertions in 7 test cases) -132: -122/235 Test #132: fpGenTestCatch ......................... Passed 0.15 sec +81: =============================================================================== +81: All tests passed (1601 assertions in 100 test cases) +81: +122/235 Test #81: fileParsersCatchTest ................... Passed 9.55 sec test 134 Start 134: pyTestMHFP 134: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 134: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 134: Test timeout computed to be: 1500 -125: Warning: Atom Count for residue ASN157A does not match expected count -117: =>start test GETAWAY custom -117: [05:51:16] test on : 365 molecules done -123/235 Test #117: testRDFcustom .......................... Passed 4.23 sec +29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +130: [15:23:17] done +130: [15:23:17] ------------------------------------- +130: [15:23:17] Test GitHub Issue #6958 +130: [15:23:17] DEPRECATION WARNING: please use AtomPairGenerator +123/235 Test #130: testFingerprintGenerators .............. Passed 1.50 sec test 135 Start 135: testPartialCharges 135: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 135: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 135: Test timeout computed to be: 1500 -124/235 Test #135: testPartialCharges ..................... Passed 0.01 sec +124/235 Test #135: testPartialCharges ..................... Passed 0.07 sec test 136 Start 136: pyPartialCharges @@ -26468,24 +26501,34 @@ 136: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 136: Test timeout computed to be: 1500 126: Warning: Atom Count for residue GLU150A does not match expected count +126: Warning: Atom Count for residue ASN157A does not match expected count +29: All 191 tests passed +29: +29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 133: .............. 133: ---------------------------------------------------------------------- -133: Ran 14 tests in 0.206s +133: Ran 14 tests in 0.351s 133: 133: OK -126: Warning: Atom Count for residue ASN157A does not match expected count -125/235 Test #133: pyTestGenerator ........................ Passed 0.64 sec +134: .. +134: ---------------------------------------------------------------------- +134: Ran 2 tests in 0.043s +134: +134: OK +125/235 Test #133: pyTestGenerator ........................ Passed 1.13 sec test 137 Start 137: testMolTransforms 137: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 137: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 137: Test timeout computed to be: 1500 -134: .. -134: ---------------------------------------------------------------------- -134: Ran 2 tests in 0.054s -134: -134: OK +126/235 Test #134: pyTestMHFP ............................. Passed 0.84 sec +test 138 + Start 138: molTransformsTestCatch + +138: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch +138: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms +138: Test timeout computed to be: 1500 137: *********************************************************** 137: Testing MolTransforms 137: --------------------------------- @@ -26516,70 +26559,83 @@ 137: testWeightedCentroid 137: 137: *********************************************************** -126/235 Test #137: testMolTransforms ...................... Passed 0.06 sec -test 138 - Start 138: molTransformsTestCatch - -138: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/molTransformsTestCatch -138: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms -138: Test timeout computed to be: 1500 -138: Randomness seeded to: 1065673637 -138: =============================================================================== -138: All tests passed (4 assertions in 1 test case) -138: -127/235 Test #138: molTransformsTestCatch ................. Passed 0.05 sec +127/235 Test #137: testMolTransforms ...................... Passed 0.11 sec test 139 Start 139: pyMolTransforms 139: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 139: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 139: Test timeout computed to be: 1500 -128/235 Test #134: pyTestMHFP ............................. Passed 0.63 sec +138: Randomness seeded to: 1463548272 +138: =============================================================================== +138: All tests passed (4 assertions in 1 test case) +138: +128/235 Test #138: molTransformsTestCatch ................. Passed 0.06 sec test 140 Start 140: forceFieldHelpersCatch 140: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/forceFieldHelpersCatch 140: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers 140: Test timeout computed to be: 1500 -81: =============================================================================== -81: All tests passed (1601 assertions in 100 test cases) -81: -129/235 Test #81: fileParsersCatchTest ................... Passed 9.38 sec +140: Randomness seeded to: 2495623965 +140: =============================================================================== +140: All tests passed (17 assertions in 2 test cases) +140: +129/235 Test #140: forceFieldHelpersCatch ................. Passed 0.05 sec test 141 Start 141: testMMFFForceFieldHelpers 141: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 141: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 141: Test timeout computed to be: 1500 -140: Randomness seeded to: 1546398637 -140: =============================================================================== -140: All tests passed (17 assertions in 2 test cases) -140: -141: [05:51:17] ------------------------------------- -141: [05:51:17] Test MMFF atom types. -130/235 Test #140: forceFieldHelpersCatch ................. Passed 0.07 sec +141: [15:23:18] ------------------------------------- +141: [15:23:18] Test MMFF atom types. +141: [15:23:18] done +141: [15:23:18] ------------------------------------- +141: [15:23:18] Testing MMFF builder tools. +141: [15:23:18] done +141: [15:23:18] ------------------------------------- +141: [15:23:18] Testing MMFF builder+minimization. +141: [15:23:18] done +141: [15:23:18] ------------------------------------- +141: [15:23:18] Testing Issue239. +136: ....... +136: ---------------------------------------------------------------------- +136: Ran 7 tests in 0.290s +136: +136: OK +141: [15:23:18] done +141: [15:23:18] ------------------------------------- +141: [15:23:18] Testing calcEnergy with passed coords. +141: [15:23:18] done +141: [15:23:18] ------------------------------------- +141: [15:23:18] Testing calcGrad. +141: [15:23:19] done +141: [15:23:19] ------------------------------------- +141: [15:23:19] Testing Issue242. +141: [15:23:19] done +141: [15:23:19] ------------------------------------- +141: [15:23:19] Testing github 308: crash during MMFF parameterization . +141: [15:23:19] ------------------------------------- +141: [15:23:19] Testing SFIssue1653802. +141: [15:23:19] done +141: [15:23:19] ------------------------------------- +141: [15:23:19] Testing SFIssue2378119. +141: [15:23:19] done +141: [15:23:19] ------------------------------------- +141: [15:23:19] Test MMFF force-field parameter getters. +141: [15:23:19] ------------------------------------- +141: [15:23:19] Test MMFF multithreading +130/235 Test #136: pyPartialCharges ....................... Passed 1.15 sec test 142 Start 142: testMMFFForceFieldHelpersMultiThread 142: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 142: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 142: Test timeout computed to be: 1500 -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing MMFF builder tools. -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing MMFF builder+minimization. -142: [05:51:17] ------------------------------------- -142: [05:51:17] Test MMFF multithreading -136: ....... -136: ---------------------------------------------------------------------- -136: Ran 7 tests in 0.158s -136: -136: OK -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing Issue239. +142: [15:23:19] ------------------------------------- +142: [15:23:19] Test MMFF multithreading +141: generating reference data 142: processing 142: launch :0 142: launch :1 @@ -26605,116 +26661,182 @@ 142: launch :21 142: launch :22 142: launch :23 -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing calcEnergy with passed coords. -131/235 Test #136: pyPartialCharges ....................... Passed 0.69 sec +142: done +142: [15:23:19] done +139: ........ +139: ---------------------------------------------------------------------- +139: Ran 8 tests in 0.250s +139: +139: OK +131/235 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.52 sec test 143 Start 143: testUFFForceFieldHelpers 143: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 143: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 143: Test timeout computed to be: 1500 -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing calcGrad. -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing Issue242. -143: [05:51:17] ------------------------------------- -143: [05:51:17] Test UFF atom labels. -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Test UFF atom typer. -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing UFF builder tools. -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing UFF builder+minimization. -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing github 308: crash during MMFF parameterization . -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing SFIssue1653802. -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Testing SFIssue2378119. -141: [05:51:17] done -141: [05:51:17] ------------------------------------- -141: [05:51:17] Test MMFF force-field parameter getters. -141: [05:51:17] ------------------------------------- -141: [05:51:17] Test MMFF multithreading -141: generating reference data -139: ........ -139: ---------------------------------------------------------------------- -139: Ran 8 tests in 0.141s -139: -139: OK -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing UFF special cases. -143: [05:51:17] UFFTYPER: Unrecognized charge state for atom: 0 -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing Issue239. -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing calcEnergy with passed coords. -142: done -132/235 Test #139: pyMolTransforms ........................ Passed 0.55 sec +117: =>start test GETAWAY custom +117: [15:23:19] test on : 365 molecules done +132/235 Test #117: testRDFcustom .......................... Passed 5.57 sec test 144 Start 144: testCrystalForceField 144: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 144: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 144: Test timeout computed to be: 1500 -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing calcGrad. -142: [05:51:17] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Test UFF atom labels. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Test UFF atom typer. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing UFF builder tools. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing UFF builder+minimization. 144: ------------------------------------- 144: Test CrystalFF torsional term. -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing SFIssue1653802. -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing SFIssue2378119. -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Test UFF force-field parameter getters. -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing handling missing parameters. -143: [05:51:17] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [05:51:17] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [05:51:17] UFFTYPER: Unrecognized hybridization for atom: 0 -143: [05:51:17] UFFTYPER: Unrecognized atom type: Cu+1 (0) -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Testing SFIssue3009337. -143: [05:51:17] done -143: [05:51:17] ------------------------------------- -143: [05:51:17] Test UFF multithreading -133/235 Test #142: testMMFFForceFieldHelpersMultiThread ... Passed 0.51 sec +133/235 Test #139: pyMolTransforms ........................ Passed 1.06 sec test 145 Start 145: pyForceFieldHelpers 145: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 145: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 145: Test timeout computed to be: 1500 +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing UFF special cases. +143: [15:23:19] UFFTYPER: Unrecognized charge state for atom: 0 +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing Issue239. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing calcEnergy with passed coords. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing calcGrad. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing SFIssue1653802. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing SFIssue2378119. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Test UFF force-field parameter getters. +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing handling missing parameters. +143: [15:23:19] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [15:23:19] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [15:23:19] UFFTYPER: Unrecognized hybridization for atom: 0 +143: [15:23:19] UFFTYPER: Unrecognized atom type: Cu+1 (0) +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Testing SFIssue3009337. +143: [15:23:19] done +143: [15:23:19] ------------------------------------- +143: [15:23:19] Test UFF multithreading 143: generating reference data -134/235 Test #144: testCrystalForceField .................. Passed 0.14 sec +134/235 Test #144: testCrystalForceField .................. Passed 0.30 sec test 146 Start 146: testDistGeomHelpers 146: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 146: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 146: Test timeout computed to be: 1500 -146: [05:51:17] ******************************************************** -146: [05:51:17] Testing DistGeomHelpers -146: [05:51:17] --------------------------------- -146: [05:51:17] test2 +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Test unfolded version of RDKFP +128: [15:23:19] ------------------------------------- +128: [15:23:19] Test bitinfo of RDKFP +128: 562: [ 2 ], +128: 709: [ 0 1 ], +128: 1118: [ 0 1 2 ], +128: 1183: [ 1 2 ], +128: 1233: [ 0 1 2 ], +128: 1308: [ 0 ], [ 1 ], +128: 1339: [ 2 ], +128: 1728: [ 1 2 ], +128: 1772: [ 0 ], [ 1 ], +128: 1813: [ 0 1 ], +128: ------------ +128: [15:23:19] ------------------------------------- +128: [15:23:19] Single atoms setting radius 1 bits in Morgan fingerprints +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Github #879: Pattern fingerprint should set bits for single-atom fragments. +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use AtomPairGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] DEPRECATION WARNING: please use TopologicalTorsionGenerator +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Github #2115: BitInfo not complete for RDKFingerprint +128: [15:23:19] done +128: [15:23:19] ------------------------------------- +128: [15:23:19] Github #3723: Fingerprint crash for mols with Zero order bonds +128: [15:23:19] done +135/235 Test #128: testFingerprints ....................... Passed 4.61 sec +test 147 + Start 147: distGeomHelpersCatch + +147: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch +147: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers +147: Test timeout computed to be: 1500 +146: [15:23:19] ******************************************************** +146: [15:23:19] Testing DistGeomHelpers +146: [15:23:19] --------------------------------- +146: [15:23:19] test2 146: 146: go 146: ------------------------------------- @@ -26724,736 +26846,448 @@ 141: launch :1 141: launch :2 141: launch :3 -141: [05:51:17] Rep: 0 Mol:1 -141: [05:51:17] Rep: 0 Mol:0 -141: [05:51:17] Rep: 0 Mol:5 -141: [05:51:17] Rep: 0 Mol:2 -141: [05:51:17] Rep: 0 Mol:9 -141: [05:51:17] Rep: 0 Mol:13 -141: [05:51:17] Rep: 0 Mol:3 -141: [05:51:17] Rep: 0 Mol:4 -141: [05:51:17] Rep: 0 Mol:17 -141: [05:51:17] Rep: 0 Mol:8 -141: [05:51:17] Rep: 0 Mol:12 -141: [05:51:17] Rep: 0 Mol:6 -141: [05:51:17] Rep: 0 Mol:10 -141: [05:51:17] Rep: 0 Mol:16 -141: [05:51:17] Rep: 0 Mol:21 -141: [05:51:17] Rep: 0 Mol:25 -141: [05:51:17] Rep: 0 Mol:7 -141: [05:51:17] Rep: 0 Mol:11 -141: [05:51:17] Rep: 0 Mol:20 +147: Randomness seeded to: 2602053797 +141: [15:23:20] Rep: 0 Mol:0 +141: [15:23:20] Rep: 0 Mol:3 +141: [15:23:20] Rep: 0 Mol:2 +141: [15:23:20] Rep: 0 Mol:4 +141: [15:23:20] Rep: 0 Mol:1 +141: [15:23:20] Rep: 0 Mol:5 +141: [15:23:20] Rep: 0 Mol:8 +141: [15:23:20] Rep: 0 Mol:9 +141: [15:23:20] Rep: 0 Mol:13 +147: [15:23:20] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] +141: [15:23:20] Rep: 0 Mol:12 +141: [15:23:20] Rep: 0 Mol:6 +141: [15:23:20] Rep: 0 Mol:16 +141: [15:23:20] Rep: 0 Mol:10 +141: [15:23:20] Rep: 0 Mol:17 +147: [15:23:20] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] +147: [15:23:20] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +147: [15:23:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [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)] +141: [15:23:20] Rep: 0 Mol:20 +147: ----------- +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [!#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)] +141: [15:23:20] Rep: 0 Mol:24 +141: [15:23:20] Rep: 0 Mol:7 +141: [15:23:20] Rep: 0 Mol:28 +147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +147: ----------- +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] 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)] +141: [15:23:20] Rep: 0 Mol:11 +141: [15:23:20] Rep: 0 Mol:15 +147: ----------- +147: ----------- +141: [15:23:20] Rep: 0 Mol:19 +141: [15:23:20] Rep: 0 Mol:21 +141: [15:23:20] Rep: 0 Mol:23 +141: [15:23:20] Rep: 0 Mol:27 +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +147: [15:23:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +141: [15:23:20] Rep: 0 Mol:31 +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +141: [15:23:20] Rep: 0 Mol:25 +145: ..[15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +141: [15:23:20] Rep: 0 Mol:29 +141: [15:23:20] Rep: 0 Mol:14 +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() 143: processing 143: launch :0 -141: [05:51:17] Rep: 0 Mol:24 143: launch :1 143: launch :2 143: launch :3 -141: [05:51:17] Rep: 0 Mol:29 -141: [05:51:17] Rep: 0 Mol:15 -141: [05:51:17] Rep: 0 Mol:19 -143: [05:51:17] Rep: 0 Mol:1 -143: [05:51:17] Rep: 0 Mol:5 -143: [05:51:17] Rep: 0 Mol:9 -143: [05:51:17] Rep: 0 Mol:0 -143: [05:51:17] Rep: 0 Mol:4 -141: [05:51:17] Rep: 0 Mol:28 -143: [05:51:17] Rep: 0 Mol:2 -143: [05:51:17] Rep: 0 Mol:3 -143: [05:51:17] Rep: 0 Mol:13 -141: [05:51:17] Rep: 0 Mol:23 -141: [05:51:17] Rep: 0 Mol:27 -141: [05:51:17] Rep: 0 Mol:31 -143: [05:51:17] Rep: 0 Mol:17 -143: [05:51:17] Rep: 0 Mol:6 -143: [05:51:17] Rep: 0 Mol:10 -143: [05:51:17] Rep: 0 Mol:8 -143: [05:51:17] Rep: 0 Mol:7 -143: [05:51:17] Rep: 0 Mol:11 -143: [05:51:17] Rep: 0 Mol:15 -143: [05:51:17] Rep: 0 Mol:21 -143: [05:51:17] Rep: 0 Mol:12 -143: [05:51:17] Rep: 0 Mol:16 -141: [05:51:17] Rep: 0 Mol:14 -143: [05:51:17] Rep: 0 Mol:19 -143: [05:51:17] Rep: 0 Mol:23 -143: [05:51:17] Rep: 0 Mol:27 -143: [05:51:17] Rep: 0 Mol:25 -143: [05:51:17] Rep: 0 Mol:14 -143: [05:51:17] Rep: 0 Mol:29 -143: [05:51:17] Rep: 0 Mol:20 -143: [05:51:17] Rep: 0 Mol:31 -143: [05:51:17] Rep: 0 Mol:18 -143: [05:51:17] Rep: 0 Mol:24 -143: [05:51:17] Rep: 0 Mol:28 -141: [05:51:18] Rep: 0 Mol:18 -143: [05:51:18] Rep: 0 Mol:22 -143: [05:51:18] Rep: 0 Mol:26 -141: [05:51:18] Rep: 0 Mol:22 -143: [05:51:18] Rep: 0 Mol:30 -141: [05:51:18] Rep: 0 Mol:26 -141: [05:51:18] Rep: 0 Mol:30 -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -141: [05:51:18] Rep: 20 Mol:0 -141: [05:51:18] Rep: 20 Mol:4 -141: [05:51:18] Rep: 20 Mol:8 -141: [05:51:18] Rep: 20 Mol:12 -141: [05:51:18] Rep: 20 Mol:16 -141: [05:51:18] Rep: 20 Mol:20 -141: [05:51:18] Rep: 20 Mol:24 -141: [05:51:18] Rep: 20 Mol:28 -145: ..[05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -141: [05:51:18] Rep: 20 Mol:1 -141: [05:51:18] Rep: 20 Mol:5 -141: [05:51:18] Rep: 20 Mol:9 -141: [05:51:18] Rep: 20 Mol:13 -141: [05:51:18] Rep: 20 Mol:17 -141: [05:51:18] Rep: 20 Mol:21 -141: [05:51:18] Rep: 20 Mol:25 -141: [05:51:18] Rep: 20 Mol:29 -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -141: [05:51:18] Rep: 20 Mol:3 -141: [05:51:18] Rep: 20 Mol:7 -141: [05:51:18] Rep: 20 Mol:11 -141: [05:51:18] Rep: 20 Mol:15 -141: [05:51:18] Rep: 20 Mol:19 -141: [05:51:18] Rep: 20 Mol:23 -141: [05:51:18] Rep: 20 Mol:27 -141: [05:51:18] Rep: 20 Mol:31 -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] UFFTYPER: Unrecognized hybridization for atom: 0 -145: [05:51:18] UFFTYPER: Unrecognized atom type: Cu+1 (0) -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: .[05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: ...[05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -145: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -141: [05:51:18] Rep: 40 Mol:0 -141: [05:51:18] Rep: 40 Mol:4 -141: [05:51:18] Rep: 40 Mol:8 -141: [05:51:18] Rep: 40 Mol:12 -141: [05:51:18] Rep: 40 Mol:16 -141: [05:51:18] Rep: 40 Mol:20 -141: [05:51:18] Rep: 40 Mol:24 -141: [05:51:18] Rep: 40 Mol:28 +143: [15:23:20] Rep: 0 Mol:2 +141: [15:23:20] Rep: 0 Mol:18 +143: [15:23:20] Rep: 0 Mol:0 +143: [15:23:20] Rep: 0 Mol:4 +143: [15:23:20] Rep: 0 Mol:1 +143: [15:23:20] Rep: 0 Mol:5 +143: [15:23:20] Rep: 0 Mol:9 +143: [15:23:20] Rep: 0 Mol:6 +143: [15:23:20] Rep: 0 Mol:10 +143: [15:23:20] Rep: 0 Mol:3 +141: [15:23:20] Rep: 0 Mol:22 +143: [15:23:20] Rep: 0 Mol:13 +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +143: [15:23:20] Rep: 0 Mol:8 +143: [15:23:20] Rep: 0 Mol:12 +143: [15:23:20] Rep: 0 Mol:16 +143: [15:23:20] Rep: 0 Mol:17 +141: [15:23:20] Rep: 0 Mol:26 +143: [15:23:20] Rep: 0 Mol:14 +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +143: [15:23:20] Rep: 0 Mol:20 +143: [15:23:20] Rep: 0 Mol:18 +143: [15:23:20] Rep: 0 Mol:24 +143: [15:23:20] Rep: 0 Mol:28 +143: [15:23:20] Rep: 0 Mol:7 +143: [15:23:20] Rep: 0 Mol:22 +143: [15:23:20] Rep: 0 Mol:11 +143: [15:23:20] Rep: 0 Mol:15 +143: [15:23:20] Rep: 0 Mol:26 +147: [15:23:20] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +141: [15:23:20] Rep: 0 Mol:30 +143: [15:23:20] Rep: 0 Mol:21 +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +143: [15:23:20] Rep: 0 Mol:19 +143: [15:23:20] Rep: 0 Mol:30 +143: [15:23:20] Rep: 0 Mol:23 +143: [15:23:20] Rep: 0 Mol:27 +143: [15:23:20] Rep: 0 Mol:25 +145: .[15:23:20] UFFTYPER: Unrecognized hybridization for atom: 0 +145: [15:23:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 1 +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[15:23:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: .[15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: ...[15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +143: [15:23:20] Rep: 0 Mol:29 +143: [15:23:20] Rep: 0 Mol:31 +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 1 +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 1 +141: [15:23:20] Rep: 20 Mol:0 +141: [15:23:20] Rep: 20 Mol:4 +141: [15:23:20] Rep: 20 Mol:8 +141: [15:23:20] Rep: 20 Mol:12 +141: [15:23:20] Rep: 20 Mol:16 +141: [15:23:20] Rep: 20 Mol:20 +141: [15:23:20] Rep: 20 Mol:24 +141: [15:23:20] Rep: 20 Mol:28 +145: [15:23:20] Molecule does not have explicit Hs. Consider calling AddHs() +141: [15:23:20] Rep: 20 Mol:3 +141: [15:23:20] Rep: 20 Mol:7 +141: [15:23:20] Rep: 20 Mol:11 +141: [15:23:20] Rep: 20 Mol:15 +141: [15:23:20] Rep: 20 Mol:19 +141: [15:23:20] Rep: 20 Mol:23 +141: [15:23:20] Rep: 20 Mol:27 +141: [15:23:20] Rep: 20 Mol:31 145: ... 145: ---------------------------------------------------------------------- -145: Ran 19 tests in 0.226s +145: Ran 19 tests in 0.281s 145: 145: OK -135/235 Test #145: pyForceFieldHelpers .................... Passed 0.86 sec -test 147 - Start 147: distGeomHelpersCatch - -147: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch -147: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers -147: Test timeout computed to be: 1500 -141: [05:51:18] Rep: 40 Mol:1 -141: [05:51:18] Rep: 40 Mol:5 -141: [05:51:18] Rep: 40 Mol:9 -141: [05:51:18] Rep: 40 Mol:13 -141: [05:51:18] Rep: 40 Mol:17 -141: [05:51:18] Rep: 40 Mol:21 -141: [05:51:18] Rep: 40 Mol:25 -141: [05:51:18] Rep: 40 Mol:29 -141: [05:51:18] Rep: 40 Mol:3 -141: [05:51:18] Rep: 40 Mol:7 -141: [05:51:18] Rep: 40 Mol:11 -141: [05:51:18] Rep: 40 Mol:15 -141: [05:51:18] Rep: 40 Mol:19 -141: [05:51:18] Rep: 40 Mol:23 -141: [05:51:18] Rep: 40 Mol:27 -141: [05:51:18] Rep: 40 Mol:31 -147: Randomness seeded to: 2237789452 -141: [05:51:18] Rep: 20 Mol:2 -141: [05:51:18] Rep: 20 Mol:6 -141: [05:51:18] Rep: 20 Mol:10 -141: [05:51:18] Rep: 20 Mol:14 -141: [05:51:18] Rep: 20 Mol:18 -141: [05:51:18] Rep: 20 Mol:22 -141: [05:51:18] Rep: 20 Mol:26 -141: [05:51:18] Rep: 20 Mol:30 -141: [05:51:18] Rep: 60 Mol:0 -141: [05:51:18] Rep: 60 Mol:4 -141: [05:51:18] Rep: 60 Mol:8 -141: [05:51:18] Rep: 60 Mol:12 -141: [05:51:18] Rep: 60 Mol:16 -141: [05:51:18] Rep: 60 Mol:20 -141: [05:51:18] Rep: 60 Mol:24 -141: [05:51:18] Rep: 60 Mol:28 -147: [05:51:18] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] -147: [05:51:18] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] -147: [05:51:18] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -147: [05:51:18] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [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)] -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -147: ----------- -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -147: ----------- -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -147: [05:51:18] [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)] -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Test unfolded version of RDKFP -128: [05:51:18] ------------------------------------- -128: [05:51:18] Test bitinfo of RDKFP -128: 562: [ 2 ], -128: 709: [ 0 1 ], -128: 1118: [ 0 1 2 ], -128: 1183: [ 1 2 ], -128: 1233: [ 0 1 2 ], -128: 1308: [ 0 ], [ 1 ], -128: 1339: [ 2 ], -128: 1728: [ 1 2 ], -128: 1772: [ 0 ], [ 1 ], -128: 1813: [ 0 1 ], -128: ------------ -128: [05:51:18] ------------------------------------- -128: [05:51:18] Single atoms setting radius 1 bits in Morgan fingerprints -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Github #879: Pattern fingerprint should set bits for single-atom fragments. -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use AtomPairGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] DEPRECATION WARNING: please use TopologicalTorsionGenerator -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Github #2115: BitInfo not complete for RDKFingerprint -128: [05:51:18] done -128: [05:51:18] ------------------------------------- -128: [05:51:18] Github #3723: Fingerprint crash for mols with Zero order bonds -128: [05:51:18] done -147: [05:51:18] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -147: ----------- -147: ----------- -136/235 Test #128: testFingerprints ....................... Passed 4.05 sec +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 5 +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 5 +141: [15:23:20] Rep: 20 Mol:1 +141: [15:23:20] Rep: 20 Mol:5 +141: [15:23:20] Rep: 20 Mol:9 +141: [15:23:20] Rep: 20 Mol:13 +141: [15:23:20] Rep: 20 Mol:17 +141: [15:23:20] Rep: 20 Mol:21 +141: [15:23:20] Rep: 20 Mol:25 +141: [15:23:20] Rep: 20 Mol:29 +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 5 +141: [15:23:20] Rep: 40 Mol:0 +141: [15:23:20] Rep: 40 Mol:4 +136/235 Test #145: pyForceFieldHelpers .................... Passed 0.94 sec test 148 Start 148: pyDistGeomHelpers 148: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 148: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 148: Test timeout computed to be: 1500 -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -147: [05:51:18] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -143: [05:51:18] Rep: 100 Mol:3 -143: [05:51:18] Rep: 100 Mol:7 -143: [05:51:18] Rep: 100 Mol:11 -143: [05:51:18] Rep: 100 Mol:15 -143: [05:51:18] Rep: 100 Mol:19 -143: [05:51:18] Rep: 100 Mol:23 -143: [05:51:18] Rep: 100 Mol:27 -143: [05:51:18] Rep: 100 Mol:31 -147: [05:51:18] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 1 -141: [05:51:18] Rep: 60 Mol:1 -141: [05:51:18] Rep: 60 Mol:5 -141: [05:51:18] Rep: 60 Mol:9 -141: [05:51:18] Rep: 60 Mol:13 -141: [05:51:18] Rep: 60 Mol:17 -141: [05:51:18] Rep: 60 Mol:21 -141: [05:51:18] Rep: 60 Mol:25 -141: [05:51:18] Rep: 60 Mol:3 -141: [05:51:18] Rep: 60 Mol:7 -141: [05:51:18] Rep: 60 Mol:11 -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 1 -143: [05:51:18] Rep: 100 Mol:0 -143: [05:51:18] Rep: 100 Mol:4 -143: [05:51:18] Rep: 100 Mol:8 -141: [05:51:18] Rep: 60 Mol:29 -141: [05:51:18] Rep: 60 Mol:15 -143: [05:51:18] Rep: 100 Mol:12 -143: [05:51:18] Rep: 100 Mol:16 -143: [05:51:18] Rep: 100 Mol:20 -143: [05:51:18] Rep: 100 Mol:24 -143: [05:51:18] Rep: 100 Mol:28 -141: [05:51:18] Rep: 60 Mol:19 -141: [05:51:18] Rep: 60 Mol:23 -141: [05:51:18] Rep: 60 Mol:27 -141: [05:51:18] Rep: 60 Mol:31 -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 1 -143: [05:51:18] Rep: 100 Mol:1 -143: [05:51:18] Rep: 100 Mol:5 -143: [05:51:18] Rep: 100 Mol:9 -143: [05:51:18] Rep: 100 Mol:13 -143: [05:51:18] Rep: 100 Mol:17 -143: [05:51:18] Rep: 100 Mol:21 -143: [05:51:18] Rep: 100 Mol:25 -143: [05:51:18] Rep: 100 Mol:29 -29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -141: [05:51:18] Rep: 80 Mol:0 -141: [05:51:18] Rep: 80 Mol:4 -141: [05:51:18] Rep: 80 Mol:8 -141: [05:51:18] Rep: 80 Mol:12 -141: [05:51:18] Rep: 80 Mol:16 -141: [05:51:18] Rep: 80 Mol:20 -141: [05:51:18] Rep: 80 Mol:24 -141: [05:51:18] Rep: 80 Mol:28 -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 5 -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 5 -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 5 -141: [05:51:18] Rep: 40 Mol:2 -141: [05:51:18] Rep: 40 Mol:6 -141: [05:51:18] Rep: 40 Mol:10 -143: [05:51:18] Rep: 100 Mol:2 -143: [05:51:18] Rep: 100 Mol:6 -143: [05:51:18] Rep: 100 Mol:10 -143: [05:51:18] Rep: 100 Mol:14 -143: [05:51:18] Rep: 100 Mol:18 -143: [05:51:18] Rep: 100 Mol:22 -143: [05:51:18] Rep: 100 Mol:26 -143: [05:51:18] Rep: 100 Mol:30 -141: [05:51:18] Rep: 40 Mol:14 -141: [05:51:18] Rep: 40 Mol:18 -141: [05:51:18] Rep: 40 Mol:22 -141: [05:51:18] Rep: 40 Mol:26 -141: [05:51:18] Rep: 40 Mol:30 -141: [05:51:18] Rep: 80 Mol:3 -141: [05:51:18] Rep: 80 Mol:7 -29: All 191 tests passed -141: [05:51:18] Rep: 80 Mol:11 -141: [05:51:18] Rep: 80 Mol:15 -141: [05:51:18] Rep: 80 Mol:19 -141: [05:51:18] Rep: 80 Mol:23 -141: [05:51:18] Rep: 80 Mol:27 -141: [05:51:18] Rep: 80 Mol:31 -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 6 -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 6 -141: [05:51:18] Rep: 80 Mol:1 -141: [05:51:18] Rep: 80 Mol:5 -141: [05:51:18] Rep: 80 Mol:9 -141: [05:51:18] Rep: 80 Mol:13 -141: [05:51:18] Rep: 80 Mol:17 -141: [05:51:18] Rep: 80 Mol:21 -141: [05:51:18] Rep: 80 Mol:25 -141: [05:51:18] Rep: 80 Mol:29 -147: [05:51:18] UFFTYPER: Unrecognized charge state for atom: 6 -29: -29: Computing MMFF94 energies for /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -148: .[05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:18] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: ..[05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -141: [05:51:19] Rep: 60 Mol:2 -141: [05:51:19] Rep: 60 Mol:6 -141: [05:51:19] Rep: 60 Mol:10 -141: [05:51:19] Rep: 60 Mol:14 -141: [05:51:19] Rep: 60 Mol:18 -141: [05:51:19] Rep: 60 Mol:22 -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -141: [05:51:19] Rep: 60 Mol:26 -141: [05:51:19] Rep: 60 Mol:30 -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -141: [05:51:19] Rep: 80 Mol:2 -141: [05:51:19] Rep: 80 Mol:6 -141: [05:51:19] Rep: 80 Mol:10 -141: [05:51:19] Rep: 80 Mol:14 -141: [05:51:19] Rep: 80 Mol:18 -141: [05:51:19] Rep: 80 Mol:22 -141: [05:51:19] Rep: 80 Mol:26 -141: [05:51:19] Rep: 80 Mol:30 -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -146: [05:51:17] --------------------------------- -146: [05:51:17] test3 -146: -146: [05:51:17] --------------------------------- -146: [05:51:17] test4 -146: -146: [05:51:17] --------------------------------- -146: [05:51:17] test5 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test6 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test15Dists -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test Issue 215 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testMultipleConfs -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testMultipleConfsExpTors -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testIssue227 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testIssue236 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testOrdering -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testIssue244 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testIssue251 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testIssue276 -146: [05:51:19] --------------------------------- -146: [05:51:19] testIssue284 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testIssue285 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testIssue355 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] testRandomCoords -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test sf.net issue 1989539 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test sf.net issue 2091864 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test constrained embedding -146: -146: [05:51:19] ssd: 0.0752641 -146: [05:51:19] ssd: 0.0659363 -143: [05:51:19] done -143: [05:51:19] ------------------------------------- -143: [05:51:19] Test UFF multithreading2 -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -146: [05:51:19] --------------------------------- -146: [05:51:19] test sf.net issue 2091974 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test sf.net issue 2835784 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test sf.net issue 3019283 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test sf.net issue 3238580 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test sf.net issue 3483968 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test github issue 55 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test1 -146: -146: [05:51:19] --------------------------------- -146: [05:51:19] test multi-threading -146: -146: building molecules -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -146: generating reference data -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -141: [05:51:19] done -141: [05:51:19] ------------------------------------- -141: [05:51:19] Test MMFF multithreading2 -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -147: [05:51:19] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: .[05:51:19] Molecule does not have explicit Hs. Consider calling AddHs() -147: [05:51:19] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -147: [05:51:20] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -148: [05:51:20] Molecule does not have explicit Hs. Consider calling AddHs() -143: [05:51:20] done -143: [05:51:20] ------------------------------------- -143: [05:51:20] Test UFF multithreading3 -147: [05:51:20] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [05:51:20] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -147: [05:51:20] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -141: [05:51:20] done -141: [05:51:20] ------------------------------------- -141: [05:51:20] Test MMFF multithreading3 -148: [05:51:20] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:20] Molecule does not have explicit Hs. Consider calling AddHs() -143: [05:51:20] done -143: [05:51:20] ------------------------------------- -143: [05:51:20] Testing GitHubIssue62. -143: [05:51:20] beta-lactam 39.6387 -143: [05:51:20] cyclopropanone 174.698 -143: [05:51:20] aziridine 337.986 -143: [05:51:20] aziridinone 115.248 -143: [05:51:20] isobutene 2.48217 -143: [05:51:20] acetone 1.91788 -143: [05:51:20] cyclopentanone 10.1648 -143: [05:51:20] cyclopropene 99.4921 -143: [05:51:20] cyclobutene 41.0156 -143: [05:51:20] cyclopropane 267.236 -143: [05:51:20] gamma-lactam 15.7471 -143: [05:51:20] trans-2,3-diphenylcyclopropan-1-one 203.398 -143: [05:51:20] cis-2,3-diphenylcyclopropan-1-one 206.852 -141: [05:51:20] done -141: [05:51:20] ------------------------------------- -141: [05:51:20] Testing github 162: Incorrect SMILES after MMFF parameterization . -141: [05:51:20] done -141: [05:51:20] ------------------------------------- -141: [05:51:20] Testing github 224: crash during MMFF parameterization . -141: [05:51:20] done -141: [05:51:20] ------------------------------------- -141: [05:51:20] Testing github6728: crash due to missing stretch-bend params. -137/235 Test #141: testMMFFForceFieldHelpers .............. Passed 4.01 sec +141: [15:23:20] Rep: 40 Mol:3 +141: [15:23:20] Rep: 40 Mol:7 +141: [15:23:20] Rep: 40 Mol:11 +141: [15:23:20] Rep: 40 Mol:15 +141: [15:23:20] Rep: 40 Mol:19 +141: [15:23:20] Rep: 40 Mol:23 +141: [15:23:20] Rep: 40 Mol:27 +141: [15:23:20] Rep: 40 Mol:31 +141: [15:23:20] Rep: 40 Mol:8 +141: [15:23:20] Rep: 40 Mol:12 +141: [15:23:20] Rep: 40 Mol:16 +141: [15:23:20] Rep: 40 Mol:20 +141: [15:23:20] Rep: 40 Mol:24 +141: [15:23:20] Rep: 40 Mol:28 +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 6 +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 6 +147: [15:23:20] UFFTYPER: Unrecognized charge state for atom: 6 +141: [15:23:20] Rep: 20 Mol:2 +141: [15:23:20] Rep: 20 Mol:6 +141: [15:23:20] Rep: 20 Mol:10 +141: [15:23:20] Rep: 20 Mol:14 +141: [15:23:20] Rep: 20 Mol:18 +141: [15:23:20] Rep: 20 Mol:22 +141: [15:23:20] Rep: 20 Mol:26 +141: [15:23:20] Rep: 20 Mol:30 +141: [15:23:20] Rep: 40 Mol:1 +141: [15:23:20] Rep: 40 Mol:5 +141: [15:23:20] Rep: 40 Mol:9 +141: [15:23:20] Rep: 40 Mol:13 +141: [15:23:20] Rep: 40 Mol:17 +141: [15:23:20] Rep: 40 Mol:21 +141: [15:23:20] Rep: 40 Mol:25 +141: [15:23:20] Rep: 40 Mol:29 +143: [15:23:20] Rep: 100 Mol:0 +143: [15:23:20] Rep: 100 Mol:4 +143: [15:23:20] Rep: 100 Mol:8 +143: [15:23:20] Rep: 100 Mol:12 +143: [15:23:20] Rep: 100 Mol:16 +141: [15:23:20] Rep: 60 Mol:3 +143: [15:23:20] Rep: 100 Mol:20 +143: [15:23:20] Rep: 100 Mol:24 +143: [15:23:20] Rep: 100 Mol:28 +141: [15:23:20] Rep: 60 Mol:7 +141: [15:23:20] Rep: 60 Mol:11 +141: [15:23:20] Rep: 60 Mol:15 +141: [15:23:20] Rep: 60 Mol:19 +141: [15:23:20] Rep: 60 Mol:23 +141: [15:23:20] Rep: 60 Mol:27 +141: [15:23:20] Rep: 60 Mol:31 +143: [15:23:20] Rep: 100 Mol:3 +143: [15:23:20] Rep: 100 Mol:7 +143: [15:23:20] Rep: 100 Mol:11 +143: [15:23:20] Rep: 100 Mol:15 +143: [15:23:20] Rep: 100 Mol:19 +143: [15:23:20] Rep: 100 Mol:23 +143: [15:23:20] Rep: 100 Mol:27 +143: [15:23:20] Rep: 100 Mol:31 +141: [15:23:20] Rep: 60 Mol:0 +141: [15:23:20] Rep: 60 Mol:4 +141: [15:23:20] Rep: 60 Mol:8 +141: [15:23:20] Rep: 60 Mol:12 +141: [15:23:20] Rep: 60 Mol:16 +141: [15:23:20] Rep: 60 Mol:20 +141: [15:23:20] Rep: 60 Mol:24 +141: [15:23:20] Rep: 60 Mol:28 +141: [15:23:20] Rep: 40 Mol:2 +141: [15:23:20] Rep: 40 Mol:6 +141: [15:23:20] Rep: 40 Mol:10 +141: [15:23:20] Rep: 40 Mol:14 +141: [15:23:20] Rep: 40 Mol:18 +141: [15:23:20] Rep: 40 Mol:22 +141: [15:23:20] Rep: 40 Mol:26 +141: [15:23:20] Rep: 40 Mol:30 +143: [15:23:20] Rep: 100 Mol:1 +143: [15:23:20] Rep: 100 Mol:5 +143: [15:23:20] Rep: 100 Mol:9 +143: [15:23:20] Rep: 100 Mol:13 +143: [15:23:20] Rep: 100 Mol:17 +143: [15:23:20] Rep: 100 Mol:21 +143: [15:23:20] Rep: 100 Mol:25 +143: [15:23:20] Rep: 100 Mol:29 +141: [15:23:21] Rep: 80 Mol:3 +141: [15:23:21] Rep: 80 Mol:7 +141: [15:23:21] Rep: 80 Mol:11 +141: [15:23:21] Rep: 80 Mol:15 +141: [15:23:21] Rep: 80 Mol:19 +141: [15:23:21] Rep: 80 Mol:23 +141: [15:23:21] Rep: 60 Mol:1 +141: [15:23:21] Rep: 60 Mol:5 +141: [15:23:21] Rep: 60 Mol:9 +141: [15:23:21] Rep: 60 Mol:13 +141: [15:23:21] Rep: 60 Mol:17 +141: [15:23:21] Rep: 60 Mol:21 +141: [15:23:21] Rep: 60 Mol:25 +141: [15:23:21] Rep: 60 Mol:29 +141: [15:23:21] Rep: 80 Mol:27 +141: [15:23:21] Rep: 80 Mol:31 +141: [15:23:21] Rep: 80 Mol:0 +141: [15:23:21] Rep: 80 Mol:4 +141: [15:23:21] Rep: 80 Mol:8 +141: [15:23:21] Rep: 60 Mol:2 +141: [15:23:21] Rep: 60 Mol:6 +141: [15:23:21] Rep: 60 Mol:10 +141: [15:23:21] Rep: 60 Mol:14 +141: [15:23:21] Rep: 60 Mol:18 +141: [15:23:21] Rep: 80 Mol:12 +141: [15:23:21] Rep: 80 Mol:16 +141: [15:23:21] Rep: 80 Mol:20 +141: [15:23:21] Rep: 80 Mol:24 +141: [15:23:21] Rep: 80 Mol:28 +141: [15:23:21] Rep: 60 Mol:22 +141: [15:23:21] Rep: 60 Mol:26 +141: [15:23:21] Rep: 60 Mol:30 +143: [15:23:21] Rep: 100 Mol:2 +143: [15:23:21] Rep: 100 Mol:6 +143: [15:23:21] Rep: 100 Mol:10 +143: [15:23:21] Rep: 100 Mol:14 +143: [15:23:21] Rep: 100 Mol:18 +143: [15:23:21] Rep: 100 Mol:22 +143: [15:23:21] Rep: 100 Mol:26 +143: [15:23:21] Rep: 100 Mol:30 +141: [15:23:21] Rep: 80 Mol:1 +141: [15:23:21] Rep: 80 Mol:5 +141: [15:23:21] Rep: 80 Mol:9 +141: [15:23:21] Rep: 80 Mol:13 +141: [15:23:21] Rep: 80 Mol:17 +141: [15:23:21] Rep: 80 Mol:21 +141: [15:23:21] Rep: 80 Mol:25 +141: [15:23:21] Rep: 80 Mol:29 +148: .[15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +95: 0,0 0 +95: 0,1 0 +95: 1,0 0 +95: 1,1 0 +95: 2,0 0 +95: 2,1 0 +141: [15:23:21] Rep: 80 Mol:2 +137/235 Test #95: testEnumeration ........................ Passed 10.85 sec test 149 Start 149: testMolAlign 149: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 149: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 149: Test timeout computed to be: 1500 -143: [05:51:20] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -143: [05:51:20] cyclopropylidencyclobutane 218.879 -143: [05:51:21] diphenylmethylidencyclobutane 79.6139 -143: [05:51:21] done -143: [05:51:21] ------------------------------------- -143: [05:51:21] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -143: [05:51:21] done -143: [05:51:21] ------------------------------------- -143: [05:51:21] Test square planar complexes -143: [05:51:21] done -143: [05:51:21] ------------------------------------- -143: [05:51:21] Test octahedral complexes -143: [05:51:21] done -138/235 Test #143: testUFFForceFieldHelpers ............... Passed 3.83 sec -test 150 - Start 150: testO3AAlign - -150: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign -150: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign -150: Test timeout computed to be: 1500 -148: [05:51:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +141: [15:23:21] Rep: 80 Mol:6 +141: [15:23:21] Rep: 80 Mol:10 +141: [15:23:21] Rep: 80 Mol:14 +141: [15:23:21] Rep: 80 Mol:18 +141: [15:23:21] Rep: 80 Mol:22 +141: [15:23:21] Rep: 80 Mol:26 +141: [15:23:21] Rep: 80 Mol:30 +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: ..[15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() 149: *********************************************************** 149: Testing MolAlign 149: --------------------------------- @@ -27475,99 +27309,293 @@ 149: testIssue241 149: 149: *********************************************************** -139/235 Test #149: testMolAlign ........................... Passed 0.19 sec -test 151 - Start 151: molAlignCatchTest +138/235 Test #149: testMolAlign ........................... Passed 0.14 sec +test 150 + Start 150: testO3AAlign -151: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest -151: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign -151: Test timeout computed to be: 1500 +150: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign +150: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign +150: Test timeout computed to be: 1500 +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +141: [15:23:21] done +141: [15:23:21] ------------------------------------- +141: [15:23:21] Test MMFF multithreading2 +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +143: [15:23:21] done +143: [15:23:21] ------------------------------------- +143: [15:23:21] Test UFF multithreading2 +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +146: [15:23:19] --------------------------------- +146: [15:23:19] test3 +146: +146: [15:23:20] --------------------------------- +146: [15:23:20] test4 +146: +146: [15:23:20] --------------------------------- +146: [15:23:20] test5 +146: +146: [15:23:21] --------------------------------- +146: [15:23:21] test6 +146: +146: [15:23:21] --------------------------------- +146: [15:23:21] test15Dists +146: +146: [15:23:21] --------------------------------- +146: [15:23:21] test Issue 215 +146: +146: [15:23:21] --------------------------------- +146: [15:23:21] testMultipleConfs +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testMultipleConfsExpTors +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testIssue227 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testIssue236 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testOrdering +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testIssue244 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testIssue251 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testIssue276 +146: [15:23:22] --------------------------------- +146: [15:23:22] testIssue284 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testIssue285 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testIssue355 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] testRandomCoords +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test sf.net issue 1989539 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test sf.net issue 2091864 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test constrained embedding +146: +146: [15:23:22] ssd: 0.0752641 +147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +146: [15:23:22] ssd: 0.0659363 +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 125: Warning: Atom Count for residue GLU5A does not match expected count 125: Warning: Atom Count for residue ASN39A does not match expected count 125: Warning: Atom Count for residue GLU53A does not match expected count 125: Warning: Atom Count for residue ARG64A does not match expected count 125: Warning: Atom Count for residue LYS80A does not match expected count +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 125: Warning: Atom Count for residue GLU150A does not match expected count 125: Warning: Atom Count for residue ASN157A does not match expected count -148: [05:51:21] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() 125: =============================================================================== 125: All tests passed (515 assertions in 10 test cases) 125: -140/235 Test #125: descriptorsTestCatch ................... Passed 7.28 sec +139/235 Test #125: descriptorsTestCatch ................... Passed 7.18 sec +test 151 + Start 151: molAlignCatchTest + +151: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest +151: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign +151: Test timeout computed to be: 1500 +147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +141: [15:23:22] done +141: [15:23:22] ------------------------------------- +141: [15:23:22] Test MMFF multithreading3 +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +151: Randomness seeded to: 3060517926 +151: 45995120 +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +146: [15:23:22] --------------------------------- +146: [15:23:22] test sf.net issue 2091974 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test sf.net issue 2835784 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test sf.net issue 3019283 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test sf.net issue 3238580 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test sf.net issue 3483968 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test github issue 55 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test1 +146: +146: [15:23:22] --------------------------------- +146: [15:23:22] test multi-threading +146: +146: building molecules +151: 72542480 +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +143: [15:23:22] done +143: [15:23:22] ------------------------------------- +143: [15:23:22] Test UFF multithreading3 +146: generating reference data +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +147: [15:23:22] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +148: [15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[15:23:22] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() +141: [15:23:23] done +141: [15:23:23] ------------------------------------- +141: [15:23:23] Testing github 162: Incorrect SMILES after MMFF parameterization . +141: [15:23:23] done +141: [15:23:23] ------------------------------------- +141: [15:23:23] Testing github 224: crash during MMFF parameterization . +141: [15:23:23] done +141: [15:23:23] ------------------------------------- +141: [15:23:23] Testing github6728: crash due to missing stretch-bend params. +140/235 Test #141: testMMFFForceFieldHelpers .............. Passed 4.47 sec test 152 Start 152: pyMolAlign 152: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 152: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap 152: Test timeout computed to be: 1500 -151: Randomness seeded to: 1819351561 -151: 43834526 -95: 0,0 0 -95: 0,1 0 -95: 1,0 0 -95: 1,1 0 -95: 2,0 0 -95: 2,1 0 -141/235 Test #95: testEnumeration ........................ Passed 12.30 sec +143: [15:23:23] done +143: [15:23:23] ------------------------------------- +143: [15:23:23] Testing GitHubIssue62. +148: [15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() +143: [15:23:23] beta-lactam 39.6387 +143: [15:23:23] cyclopropanone 174.698 +143: [15:23:23] aziridine 337.986 +143: [15:23:23] aziridinone 115.248 +143: [15:23:23] isobutene 2.48217 +143: [15:23:23] acetone 1.91788 +143: [15:23:23] cyclopentanone 10.1648 +143: [15:23:23] cyclopropene 99.4921 +143: [15:23:23] cyclobutene 41.0156 +143: [15:23:23] cyclopropane 267.236 +143: [15:23:23] gamma-lactam 15.7471 +143: [15:23:23] trans-2,3-diphenylcyclopropan-1-one 203.398 +143: [15:23:23] cis-2,3-diphenylcyclopropan-1-one 206.852 +143: [15:23:23] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +143: [15:23:23] cyclopropylidencyclobutane 218.879 +143: [15:23:23] diphenylmethylidencyclobutane 79.6139 +143: [15:23:23] done +143: [15:23:23] ------------------------------------- +143: [15:23:23] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +143: [15:23:23] done +143: [15:23:23] ------------------------------------- +143: [15:23:23] Test square planar complexes +143: [15:23:23] done +143: [15:23:23] ------------------------------------- +143: [15:23:23] Test octahedral complexes +143: [15:23:23] done +141/235 Test #143: testUFFForceFieldHelpers ............... Passed 3.85 sec test 153 Start 153: testFeatures 153: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 153: Test timeout computed to be: 1500 -151: 53929553 -153: [05:51:21] ------------------------------------- -153: [05:51:21] AtomType parser testing. -153: [05:51:21] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -153: [05:51:21] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] FeatureDefinition parser testing. -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Test pulling feat defs from a string. -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] FeatureDef functionality testing. -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] FeatureFactory testing. -153: [05:51:21] 1 -153: [05:51:21] 2 -153: [05:51:21] 3 -153: [05:51:21] 4 -153: [05:51:21] 5 -153: [05:51:21] 6 -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Feature Location testing. -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Test building a FeatureFactory from a file -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Testing Issue 224. -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Testing Issue 225. -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Test Issue346 -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Test Issue347 -153: [05:51:21] done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Testing Issue 348. -153: [05:51:21] SMARTS Parse Error: syntax error while parsing: [C[C] -153: [05:51:21] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -153: [05:51:21] ------------------------------------- -153: [05:51:21] Testing Nested AtomType definitions. +153: [15:23:23] ------------------------------------- +153: [15:23:23] AtomType parser testing. +153: [15:23:23] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +153: [15:23:23] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] FeatureDefinition parser testing. +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Test pulling feat defs from a string. +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] FeatureDef functionality testing. +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] FeatureFactory testing. +153: [15:23:23] 1 +153: [15:23:23] 2 +153: [15:23:23] 3 +153: [15:23:23] 4 +153: [15:23:23] 5 +153: [15:23:23] 6 +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Feature Location testing. +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Test building a FeatureFactory from a file +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Testing Issue 224. +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Testing Issue 225. +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Test Issue346 +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Test Issue347 +153: [15:23:23] done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Testing Issue 348. +153: [15:23:23] SMARTS Parse Error: syntax error while parsing: [C[C] +153: [15:23:23] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +153: [15:23:23] ------------------------------------- +153: [15:23:23] Testing Nested AtomType definitions. 153: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -153: [05:51:21] ------------------------------------- -153: [05:51:21] Testing Github Issue #252: crash when calling getPos() with no conformer. -153: [05:51:21] expect a precondition failure message below -153: [05:51:21] +153: [15:23:23] ------------------------------------- +153: [15:23:23] Testing Github Issue #252: crash when calling getPos() with no conformer. +153: [15:23:23] expect a precondition failure message below +153: [15:23:23] 153: 153: **** 153: Pre-condition Violation @@ -27580,37 +27608,31 @@ 153: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 153: 2# RDKit::MolChemicalFeature::getPos(int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 153: 3# RDKit::MolChemicalFeature::getPos() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolChemicalFeatures.so.1 -153: 4# 0x0000AAAAE54D1AB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 5# 0x0000AAAAE54C4568 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures -153: 6# 0x0000FFFF84A4229C in /lib/aarch64-linux-gnu/libc.so.6 +153: 4# 0x0000AAAAD3C51AB0 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 5# 0x0000AAAAD3C44568 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 6# 0x0000FFFFA541229C in /lib/aarch64-linux-gnu/libc.so.6 153: 7# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -153: 8# 0x0000AAAAE54C4730 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures +153: 8# 0x0000AAAAD3C44730 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 153: ---------- 153: **** 153: -153: [05:51:21] Done -153: [05:51:21] ------------------------------------- -153: [05:51:21] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -153: [05:51:21] done -142/235 Test #153: testFeatures ........................... Passed 0.03 sec +153: [15:23:23] Done +153: [15:23:23] ------------------------------------- +153: [15:23:23] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +153: [15:23:23] done +142/235 Test #153: testFeatures ........................... Passed 0.06 sec test 154 Start 154: pyChemicalFeatures 154: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 154: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 154: Test timeout computed to be: 1500 -154: .[05:51:21] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[05:51:21] Molecule does not have explicit Hs. Consider calling AddHs() -154: ..[05:51:21] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[05:51:21] Molecule does not have explicit Hs. Consider calling AddHs() -154: .[05:51:21] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -154: [05:51:21] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -154: ... -154: ---------------------------------------------------------------------- -154: Ran 9 tests in 0.064s -154: -154: OK -143/235 Test #154: pyChemicalFeatures ..................... Passed 0.44 sec +148: [15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() +52: Randomness seeded to: 1674199327 +52: =============================================================================== +52: All tests passed (14835 assertions in 14 test cases) +52: +143/235 Test #52: canonTestsCatch ........................ Passed 18.46 sec test 155 Start 155: testShapeHelpers @@ -27629,14 +27651,13 @@ 155: testGithub4364 155: 155: *********************************************************** -144/235 Test #155: testShapeHelpers ....................... Passed 0.03 sec +144/235 Test #155: testShapeHelpers ....................... Passed 0.05 sec test 156 Start 156: pyShapeHelpers 156: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 156: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 156: Test timeout computed to be: 1500 -146: validating reference data 126: Warning: Atom Count for residue GLU5A does not match expected count 126: Warning: Atom Count for residue ASN39A does not match expected count 126: Warning: Atom Count for residue GLU53A does not match expected count @@ -27644,59 +27665,58 @@ 126: Warning: Atom Count for residue LYS80A does not match expected count 126: Warning: Atom Count for residue GLU150A does not match expected count 126: Warning: Atom Count for residue ASN157A does not match expected count -148: [05:51:21] Molecule does not have explicit Hs. Consider calling AddHs() -126: .[05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: .[05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: ..[05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: .[05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ...[05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: [05:51:21] DEPRECATION WARNING: please use MorganGenerator -126: ....[05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: ....[05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: [05:51:21] DEPRECATION WARNING: please use AtomPairGenerator -126: .[05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: ..[05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: .[05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator -126: [05:51:21] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: .[15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: ..[15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: .[15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ...[15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: [15:23:23] DEPRECATION WARNING: please use MorganGenerator +126: ....[15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: ....[15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: [15:23:23] DEPRECATION WARNING: please use AtomPairGenerator +126: .[15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: ..[15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: .[15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator +126: [15:23:23] DEPRECATION WARNING: please use TopologicalTorsionGenerator 126: ... 126: ---------------------------------------------------------------------- -126: Ran 31 tests in 7.157s +126: Ran 31 tests in 8.276s 126: 126: OK 126: exactmw 78.046950192 @@ -27745,8 +27765,10 @@ 126: CustomNumAtoms 6.0 126: exactmw 78.046950192 126: lipinskiHBA 0.0 -148: [05:51:22] Molecule does not have explicit Hs. Consider calling AddHs() -145/235 Test #126: pyMolDescriptors ....................... Passed 8.04 sec +148: [15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[15:23:23] Molecule does not have explicit Hs. Consider calling AddHs() +145/235 Test #126: pyMolDescriptors ....................... Passed 8.80 sec test 157 Start 157: testMolCatalog @@ -27760,9 +27782,19 @@ 158: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 158: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 158: Test timeout computed to be: 1500 +148: [15:23:24] Molecule does not have explicit Hs. Consider calling AddHs() +154: ..[15:23:24] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[15:23:24] Molecule does not have explicit Hs. Consider calling AddHs() +154: .[15:23:24] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +154: [15:23:24] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +154: ... +154: ---------------------------------------------------------------------- +154: Ran 9 tests in 0.132s +154: +154: OK 156: . 156: ---------------------------------------------------------------------- -156: Ran 1 test in 0.054s +156: Ran 1 test in 0.065s 156: 156: OK 156: Testing Shape Helpers wrapper @@ -27773,13 +27805,20 @@ 159: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 159: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 159: Test timeout computed to be: 1500 -148: [05:51:22] Molecule does not have explicit Hs. Consider calling AddHs() 159: ----------------- Test 1 +148/235 Test #154: pyChemicalFeatures ..................... Passed 0.67 sec +test 160 + Start 160: moldraw2DTestCatch + +160: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +160: Test timeout computed to be: 1500 159: file test1_6.svg gave hash 1109656969U not the expected 2635907956U 159: Done 159: ----------------- Test 2 159: file test2_1.png gave hash 2906135263U not the expected 638584804U 159: file test2_2.png gave hash 1323626475U not the expected 610424244U +146: validating reference data 159: file test2_3.png gave hash 2294574389U not the expected 2179746375U 159: Done 159: ----------------- Test 4 @@ -27794,59 +27833,85 @@ 159: Done 159: ----------------- Test 7 (backgrounds) 159: file test7_1.png gave hash 3442107642U not the expected 1322246680U +160: Randomness seeded to: 3614402425 +160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U +160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U 159: file test7_2.png gave hash 2446896946U not the expected 1499012715U 159: Done 159: ----------------- Test8: PrepareMolDrawing 159: Done 159: ----------------- Test multi-threaded drawing 159: reading molecules -151: 1162578677 -148: [05:51:22] Molecule does not have explicit Hs. Consider calling AddHs() +160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U +160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U +160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U 159: generating reference drawings +160: file testGithub3226_1.png gave hash 2884766435U not the expected 3165135374U +160: file testGithub3226_2.png gave hash 2496669020U not the expected 643975155U +160: file testGithub3226_3.png gave hash 3470350919U not the expected 3119571946U +151: 1875210760 +160: file testPNGMetadata_1.png gave hash 3544974138U not the expected 997629701U 159: processing 159: launch :0 159: launch :1 159: launch :2 159: launch :3 +160: file testPNGMetadata_2.png gave hash 2226910827U not the expected 1797853056U +160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U +160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-1.png gave hash 2532617830U not the expected 3894611804U +29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 158: . 158: ---------------------------------------------------------------------- -158: Ran 1 test in 0.014s +158: Ran 1 test in 0.050s 158: 158: OK -148: [05:51:22] Molecule does not have explicit Hs. Consider calling AddHs() -148/235 Test #158: pyMolCatalog ........................... Passed 0.61 sec -test 160 - Start 160: moldraw2DTestCatch - -160: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -160: Test timeout computed to be: 1500 -160: Randomness seeded to: 403957139 -160: file contourMol_1.svg gave hash 4125787245U not the expected 3634867913U -160: file contourMol_2.svg gave hash 2761342533U not the expected 1815941817U -160: file contourMol_3.svg gave hash 1333854566U not the expected 2579392727U -160: file contourMol_4.svg gave hash 4249475618U not the expected 2914799663U -160: file contourMol_5.svg gave hash 3376179346U not the expected 3792684719U -148: [05:51:23] Molecule does not have explicit Hs. Consider calling AddHs() -151: 511031259 -151: =============================================================================== -151: All tests passed (73 assertions in 3 test cases) -151: -160: file testGithub3226_1.png gave hash 2884766435U not the expected 3165135374U -149/235 Test #151: molAlignCatchTest ...................... Passed 1.89 sec +160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-2.svg gave hash 700659102U not the expected 794717511U +160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-2.png gave hash 1194644863U not the expected 1443443188U +160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U +160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-3.png gave hash 3369355742U not the expected 865629432U +160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U +160: [15:23:24] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:24] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-4.png gave hash 1247155982U not the expected 3919767093U +149/235 Test #158: pyMolCatalog ........................... Passed 0.70 sec test 161 Start 161: moldraw2DRxnTest1 161: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 161: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 161: Test timeout computed to be: 1500 -160: file testGithub3226_2.png gave hash 2496669020U not the expected 643975155U -160: file testGithub3226_3.png gave hash 3470350919U not the expected 3119571946U +29: All 191 tests passed +29: done +29: ------------------------------------- +29: Unit tests for all MMFF constraint terms. 161: ----------------- Test 1 -160: file testPNGMetadata_1.png gave hash 3544974138U not the expected 997629701U +29: 10.0003 161: file rxn_test1_1.png gave hash 169116773U not the expected 801892091U +29: done +29: ------------------------------------- +29: Unit test for MMFF TorsionConstraint close to 0 degrees. +29: done +29: ------------------------------------- +29: Unit tests for copying MMFF ForceFields. +29: done +29: ------------------------------------- +29: Unit test for MMFF butane scan. 161: file rxn_test1_2.png gave hash 1054415001U not the expected 507435337U -160: file testPNGMetadata_2.png gave hash 2226910827U not the expected 1797853056U +148: [15:23:24] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test1_3.png gave hash 1401039782U not the expected 1590809137U 161: file rxn_test1_4.png gave hash 1077411151U not the expected 1766700542U 161: file rxn_test1_5.png gave hash 1082898052U not the expected 2552100594U @@ -27854,20 +27919,34 @@ 161: file rxn_test1_7.png gave hash 2659385921U not the expected 1461397406U 161: Done 161: ----------------- Test 2: some examples that caused problems in testing -160: [05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U -160: [05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test2_1.png gave hash 2159157032U not the expected 3551633840U +148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C 161: file rxn_test2_2_1.png gave hash 558529985U not the expected 1268122583U 161: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl -160: file testHandDrawn-1.png gave hash 2532617830U not the expected 3894611804U +151: 633441040 +151: =============================================================================== +151: All tests passed (73 assertions in 3 test cases) +151: +150/235 Test #151: molAlignCatchTest ...................... Passed 2.75 sec +test 162 + Start 162: pyMolDraw2D + +162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" +162: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap +162: Test timeout computed to be: 1500 161: file rxn_test2_2_2.png gave hash 431249733U not the expected 82821108U 161: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 161: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 161: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C +29: done +151/235 Test #29: testMMFFForceField ..................... Passed 21.05 sec +test 163 + Start 163: testFMCS + +163: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS +163: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS +163: Test timeout computed to be: 1500 161: file rxn_test2_2_3.png gave hash 4183177411U not the expected 3828365604U 161: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC 161: file rxn_test2_2_4.png gave hash 798840480U not the expected 1230108677U @@ -27877,38 +27956,22 @@ 161: Done 161: ----------------- Test 4: some examples from SMARTS in testing 161: draw! -160: [05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 161: file rxn_test4_1.png gave hash 1538512166U not the expected 2745201873U 161: done -160: file testHandDrawn-2.svg gave hash 700659102U not the expected 794717511U -160: [05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 161: file rxn_test4_2.png gave hash 4290002109U not the expected 3094925886U +148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 161: Done -160: file testHandDrawn-2.png gave hash 1194644863U not the expected 1443443188U -160: [05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-3.svg gave hash 2359787964U not the expected 3982694296U -160: [05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -150/235 Test #161: moldraw2DRxnTest1 ...................... Passed 0.37 sec -test 162 - Start 162: pyMolDraw2D +152/235 Test #161: moldraw2DRxnTest1 ...................... Passed 0.77 sec +test 164 + Start 164: pyFMCS -162: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" -162: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap -162: Test timeout computed to be: 1500 -160: file testHandDrawn-3.png gave hash 3369355742U not the expected 865629432U -160: [05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-4.svg gave hash 1880974760U not the expected 2146113517U -160: [05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -160: file testHandDrawn-4.png gave hash 1247155982U not the expected 3919767093U -162: ...[05:51:23] Font file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -162: [05:51:23] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -162: ..........[05:51:23] +164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap/testFMCS.py" +164: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap +164: Test timeout computed to be: 1500 +162: ...[15:23:25] Font file /build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +162: [15:23:25] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +162: ..........[15:23:25] 162: 162: **** 162: Pre-condition Violation @@ -27922,7 +27985,7 @@ 162: 2# RDKit::prepMolForDrawing(RDKit::ROMol const*, bool, bool, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector7 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/Draw/rdMolDraw2D.so 162: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -162: 5# 0x0000FFFFB3882680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 5# 0x0000FFFFADB72680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 162: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdDepictor.so @@ -27933,17 +27996,17 @@ 162: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 162: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 162: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 16# 0x0000FFFFB2E9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 17# 0x0000FFFFB2E9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 18# 0x0000FFFFB2E9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 19# 0x0000FFFFB2E9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -162: 20# 0x0000FFFFB2E9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 16# 0x0000FFFFAD18B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 17# 0x0000FFFFAD18B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 18# 0x0000FFFFAD18B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 19# 0x0000FFFFAD18B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +162: 20# 0x0000FFFFAD18B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 162: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 162: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -162: 26# 0x0000FFFFB387F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +162: 26# 0x0000FFFFADB6F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 162: 27# _PyObject_MakeTpCall in /usr/bin/python3 162: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 162: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -27975,70 +28038,35 @@ 162: 55# 0x0000000000627010 in /usr/bin/python3 162: 56# Py_RunMain in /usr/bin/python3 162: 57# Py_BytesMain in /usr/bin/python3 -162: 58# 0x0000FFFFB51A229C in /lib/aarch64-linux-gnu/libc.so.6 +162: 58# 0x0000FFFFAF49229C in /lib/aarch64-linux-gnu/libc.so.6 162: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 162: 60# _start in /usr/bin/python3 162: ---------- 162: **** 162: +148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 146: processing 146: launch :0 146: launch :1 146: launch :2 146: launch :3 -148: .[05:51:23] Molecule does not have explicit Hs. Consider calling AddHs() +160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U +160: [15:23:25] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:25] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. +160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U +160: [15:23:25] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. +160: [15:23:25] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. 162: ...................... 162: ---------------------------------------------------------------------- -162: Ran 35 tests in 0.263s +162: Ran 35 tests in 0.277s 162: 162: OK 162: json lasso -52: Randomness seeded to: 1410133053 -52: =============================================================================== -52: All tests passed (14835 assertions in 14 test cases) -52: -151/235 Test #52: canonTestsCatch ........................ Passed 18.57 sec -test 163 - Start 163: testFMCS - -163: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS -163: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS -163: Test timeout computed to be: 1500 -152/235 Test #162: pyMolDraw2D ............................ Passed 0.68 sec -test 164 - Start 164: pyFMCS - -164: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/FMCS/Wrap/testFMCS.py" -164: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap -164: Test timeout computed to be: 1500 -29: Checking against /build/reproducible-path/rdkit-202409.6/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -29: All 191 tests passed -29: done -29: ------------------------------------- -29: Unit tests for all MMFF constraint terms. -160: file testHandDrawn-5a.svg gave hash 2796249138U not the expected 1567781555U -160: [05:51:25] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:25] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -29: 10.0003 -160: file testHandDrawn-5b.svg gave hash 4043231252U not the expected 66354106U -160: [05:51:25] Font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/ComicNeue-Regular.ttf not found. -160: [05:51:25] Falling back to original font file /build/reproducible-path/rdkit-202409.6/Data/Fonts/Telex-Regular.ttf. -29: done -29: ------------------------------------- -29: Unit test for MMFF TorsionConstraint close to 0 degrees. -29: done -29: ------------------------------------- -29: Unit tests for copying MMFF ForceFields. -29: done -29: ------------------------------------- -29: Unit test for MMFF butane scan. 160: file testHandDrawn-5.png gave hash 2430523987U not the expected 828378555U 160: file testBrackets-5a.svg gave hash 279553678U not the expected 1447240271U +148: [15:23:25] Molecule does not have explicit Hs. Consider calling AddHs() 160: file testPositionVariation-1b.svg gave hash 3055422087U not the expected 3269244452U -160: [05:51:25] unrecognized bond typefile testGithub4238_1.png gave hash 4081567765U not the expected 2623427676U -160: file testGithub4323_1.png gave hash 3210012906U not the expected 3075787867U -29: done -153/235 Test #29: testMMFFForceField ..................... Passed 20.95 sec +153/235 Test #162: pyMolDraw2D ............................ Passed 0.85 sec test 165 Start 165: FMCStest @@ -30010,26 +30038,26 @@ 165: 165: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 165: ERROR: RDKit could not load input file -154/235 Test #165: FMCStest ............................... Passed 0.10 sec +154/235 Test #165: FMCStest ............................... Passed 0.05 sec test 166 Start 166: molHashCatchTest 166: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 166: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 166: Test timeout computed to be: 1500 -166: Randomness seeded to: 168039159 +160: [15:23:26] unrecognized bond typefile testGithub4238_1.png gave hash 4081567765U not the expected 2623427676U +160: file testGithub4323_1.png gave hash 3210012906U not the expected 3075787867U +166: Randomness seeded to: 1678077751 166: =============================================================================== 166: All tests passed (363 assertions in 14 test cases) 166: -155/235 Test #166: molHashCatchTest ....................... Passed 0.11 sec +155/235 Test #166: molHashCatchTest ....................... Passed 0.13 sec test 167 Start 167: pyMolHash 167: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolHash/Wrap/testMolHash.py" 167: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 167: Test timeout computed to be: 1500 -160: file testGithub4323_3.png gave hash 2585216301U not the expected 381907253U -160: [05:51:25] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 150: *********************************************************** 150: Testing O3AAlign 150: --------------------------------- @@ -30060,21 +30088,94 @@ 150: testMMFFO3A multithreading 150: 150: generating reference data +160: file testGithub4323_3.png gave hash 2585216301U not the expected 381907253U +160: [15:23:26] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 167: .... 167: ---------------------------------------------------------------------- -167: Ran 4 tests in 0.017s +167: Ran 4 tests in 0.020s 167: 167: OK -156/235 Test #167: pyMolHash .............................. Passed 0.45 sec +156/235 Test #167: pyMolHash .............................. Passed 0.63 sec test 168 Start 168: testMMPA 168: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/testMMPA 168: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA 168: Test timeout computed to be: 1500 +163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: test32() +163: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds +163: Time elapsed 0.070 seconds +163: +163: test190() +163: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds +163: Time elapsed 0.009 seconds +163: +163: test3() +163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds +163: Time elapsed 0.015 seconds +163: +163: testSimpleFast() +163: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds +163: Time elapsed 0.088 seconds +163: +163: testSimple() +163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +163: Time elapsed 0.051 seconds +163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +163: Time elapsed 0.073 seconds +163: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +163: Time elapsed 0.126 seconds +163: +163: testSegFault() +163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.009 seconds +163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.015 seconds +163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds +163: Time elapsed 0.015 seconds +163: +163: testThreshold() +163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +163: Time elapsed 0.000 seconds +163: +163: testRing1() +163: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds +163: Time elapsed 0.349 seconds +163: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds +163: Time elapsed 0.347 seconds +163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds +163: Time elapsed 0.385 seconds +163: +163: testAtomCompareIsotopes() +163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +163: Time elapsed 0.000 seconds +163: +163: testAtomCompareAnyAtom() +163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +163: Time elapsed 0.000 seconds +163: +163: testJnk1LigandsDistance() +163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds +163: Time elapsed 0.005 seconds +163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002241 seconds +168: Time elapsed 0.002254 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -30111,11 +30212,12 @@ 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. +148: .[15:23:26] Molecule does not have explicit Hs. Consider calling AddHs() 168: 168: --- UNMATCHED Reference RESULTS: --- 168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 168: ----------------------------------- -168: Time elapsed 0.002944 seconds +168: Time elapsed 0.001954 seconds 168: 168: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 168: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -30157,7 +30259,7 @@ 168: ----------------------------------- 168: 168: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -168: Time elapsed 0.002692 seconds +168: Time elapsed 0.001967 seconds 168: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 168: 1: PASSED. matchedRefRes = 4 168: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] @@ -30197,7 +30299,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -168: Time elapsed 0.000571 seconds +168: Time elapsed 0.012640 seconds 168: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 168: 1: PASSED. matchedRefRes = 2 168: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -30219,7 +30321,7 @@ 168: ----------------------------------- 168: 168: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -168: Time elapsed 0.002102 seconds +168: Time elapsed 0.002137 seconds 168: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 168: 1: NOREF. Reference data NOT LISTED in test case. 168: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -30242,6 +30344,7 @@ 168: 10: NOREF. Reference data NOT LISTED in test case. 168: 11: res= C[C:0](C(=O)N[*:2])[*:1],C1CC[NH+]([*:1])C1.Cc1ccccc1[*:2] 168: 11: NOREF. Reference data NOT LISTED in test case. +160: file testFlexiCanvas.2a.png gave hash 2206969409U not the expected 2609920321U 168: 12: res= NULL,C[C:2]([NH+]1CCCC1)[*:1].Cc1ccccc1NC(=O)[*:1] 168: 12: NOREF. Reference data NOT LISTED in test case. 168: 13: res= C1CC[NH+]([C:0]([*:1])[*:2])C1,C[*:1].Cc1ccccc1NC(=O)[*:2] @@ -30256,158 +30359,22 @@ 168: 17: NOREF. Reference data NOT LISTED in test case. 168: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 168: 18: NOREF. Reference data NOT LISTED in test case. -168: -168: --- UNMATCHED Reference RESULTS: --- -168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] -168: ----------------------------------- -168: -168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -168: Time elapsed 0.002261 seconds -168: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 -168: 1: NOREF. Reference data NOT LISTED in test case. -168: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 -168: 2: NOREF. Reference data NOT LISTED in test case. -168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 -168: 3: NOREF. Reference data NOT LISTED in test case. -168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 -168: 4: NOREF. Reference data NOT LISTED in test case. -168: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 -168: 5: NOREF. Reference data NOT LISTED in test case. -168: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 -168: 6: NOREF. Reference data NOT LISTED in test case. -168: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 -168: 7: NOREF. Reference data NOT LISTED in test case. -168: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 -168: 8: NOREF. Reference data NOT LISTED in test case. -168: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 -168: 9: NOREF. Reference data NOT LISTED in test case. -168: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 -168: 10: NOREF. Reference data NOT LISTED in test case. -168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 -168: 11: NOREF. Reference data NOT LISTED in test case. -168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] -168: 12: NOREF. Reference data NOT LISTED in test case. -168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] -168: 13: NOREF. Reference data NOT LISTED in test case. -168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 -168: 14: PASSED. matchedRefRes = 1 -168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 -168: 15: NOREF. Reference data NOT LISTED in test case. -168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] -168: 16: NOREF. Reference data NOT LISTED in test case. -168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 -168: 17: NOREF. Reference data NOT LISTED in test case. -168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 -168: 18: NOREF. Reference data NOT LISTED in test case. -168: -168: --- ALL PASSED --- -168: ----------------------------------- -168: 5 TEST CASES FAILED -157/235 Test #168: testMMPA ............................... Passed 0.15 sec -test 169 - Start 169: pyMMPA - -169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/testMMPA.py" -169: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap -169: Test timeout computed to be: 1500 -160: file testFlexiCanvas.2a.png gave hash 2206969409U not the expected 2609920321U 160: file testFlexiCanvas.2b.png gave hash 2563070594U not the expected 3615599154U -160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -160: file testGithub4764.sz1.png gave hash 434772931U not the expected 2179222277U -163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: test32() -163: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds -163: Time elapsed 0.107 seconds -163: -163: test190() -163: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds -163: Time elapsed 0.013 seconds -163: -163: test3() -163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -163: Time elapsed 0.024 seconds -163: -163: testSimpleFast() -163: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds -163: Time elapsed 0.170 seconds -163: -163: testSimple() -163: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.157 seconds -163: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.177 seconds -163: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -163: Time elapsed 0.181 seconds -163: -163: testSegFault() -163: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.013 seconds -163: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.023 seconds -163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds -163: Time elapsed 0.023 seconds -163: -163: testThreshold() -163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -163: Time elapsed 0.000 seconds -163: -163: testRing1() -163: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -163: Time elapsed 0.527 seconds -163: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -163: Time elapsed 0.511 seconds -163: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds -163: Time elapsed 0.576 seconds -163: -163: testAtomCompareIsotopes() -163: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -163: Time elapsed 0.000 seconds -163: -163: testAtomCompareAnyAtom() -163: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -163: Time elapsed 0.000 seconds -163: -163: testJnk1LigandsDistance() -163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds -163: Time elapsed 0.009 seconds -163: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds -160: file testGithub4764.sz2.png gave hash 3567858909U not the expected 444262090U -160: file testGithub4764.sz3.png gave hash 3541535490U not the expected 3567162200U -160: file github5383_1.svg gave hash 2761342533U not the expected 1815941817U -160: file github5383_2.svg gave hash 2560846108U not the expected 0U -160: file github5383_1.png gave hash 186818321U not the expected 2893520928U -160: file acs1996_1.png gave hash 1116230394U not the expected 2329725800U 163: Time elapsed 0.001 seconds 163: 163: test18() 163: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 163: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds -163: Time elapsed 0.004 seconds +163: Time elapsed 0.008 seconds 163: 163: test504() 163: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 163: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds -163: Time elapsed 0.144 seconds +163: Time elapsed 0.102 seconds 163: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 163: Time elapsed 0.001 seconds 163: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds -163: Time elapsed 0.038 seconds +163: Time elapsed 0.030 seconds 163: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds 163: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0009 seconds. bond[0]=6 163: STATISTICS: @@ -30471,6 +30438,25 @@ 163: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds 163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 163: res sub = 1 size=4 +168: +168: --- UNMATCHED Reference RESULTS: --- +168: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] +168: ----------------------------------- +168: +168: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 +168: Time elapsed 0.010509 seconds +168: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 +168: 1: NOREF. Reference data NOT LISTED in test case. +168: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 +168: 2: NOREF. Reference data NOT LISTED in test case. +168: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 +168: 3: NOREF. Reference data NOT LISTED in test case. +168: 4: res= O=C(O[*:1])C(c1ccccc1)[*:2],O[*:2].c1ccc(C[*:1])cc1 +168: 4: NOREF. Reference data NOT LISTED in test case. +168: 5: res= O=C(O[*:1])C([*:2])[*:3],O[*:2].c1ccc(C[*:1])cc1.c1ccc([*:3])cc1 +168: 5: NOREF. Reference data NOT LISTED in test case. +168: 6: res= O=C(O[*:1])C(O)[*:2],c1ccc(C[*:1])cc1.c1ccc([*:2])cc1 +168: 6: NOREF. Reference data NOT LISTED in test case. 163: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds 163: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 163: res sub = 1 size=4 @@ -30526,28 +30512,73 @@ 163: res sub = 1 size=3 163: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: done +168: 7: res= NULL,O=C(OC[*:1])C(O)c1ccccc1.c1ccc([*:1])cc1 +168: 7: NOREF. Reference data NOT LISTED in test case. +168: 8: res= O=C(OC[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc([*:2])cc1 +168: 8: NOREF. Reference data NOT LISTED in test case. +168: 9: res= O=C(OC[*:2])C(c1ccccc1)[*:1],O[*:1].c1ccc([*:2])cc1 +168: 9: NOREF. Reference data NOT LISTED in test case. +168: 10: res= O=C(OC[*:2])C([*:1])[*:3],O[*:1].c1ccc([*:2])cc1.c1ccc([*:3])cc1 +168: 10: NOREF. Reference data NOT LISTED in test case. +168: 11: res= O=C(OC[*:1])C(O)[*:2],c1ccc([*:1])cc1.c1ccc([*:2])cc1 +168: 11: NOREF. Reference data NOT LISTED in test case. +168: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] +168: 12: NOREF. Reference data NOT LISTED in test case. +168: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] +168: 13: NOREF. Reference data NOT LISTED in test case. +168: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 +168: 14: PASSED. matchedRefRes = 1 +168: 15: res= OC([*:1])[*:2],O=C(OCc1ccccc1)[*:1].c1ccc([*:2])cc1 +168: 15: NOREF. Reference data NOT LISTED in test case. +168: 16: res= NULL,O=C(OCc1ccccc1)C(c1ccccc1)[*:1].O[*:1] +168: 16: NOREF. Reference data NOT LISTED in test case. +168: 17: res= O=C(OCc1ccccc1)C([*:1])[*:2],O[*:1].c1ccc([*:2])cc1 +168: 17: NOREF. Reference data NOT LISTED in test case. +168: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 +168: 18: NOREF. Reference data NOT LISTED in test case. +168: +168: --- ALL PASSED --- +168: ----------------------------------- +168: 5 TEST CASES FAILED +157/235 Test #168: testMMPA ............................... Passed 0.24 sec +test 169 + Start 169: pyMMPA + +169: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MMPA/Wrap/testMMPA.py" +169: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap +169: Test timeout computed to be: 1500 +160: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +160: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +160: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U +160: file testGithub4764.sz1.png gave hash 434772931U not the expected 2179222277U +160: file testGithub4764.sz2.png gave hash 3567858909U not the expected 444262090U +160: file testGithub4764.sz3.png gave hash 3541535490U not the expected 3567162200U +160: file github5383_1.svg gave hash 2761342533U not the expected 1815941817U +160: file github5383_2.svg gave hash 2560846108U not the expected 0U +160: file github5383_1.png gave hash 186818321U not the expected 2893520928U +160: file acs1996_1.png gave hash 1116230394U not the expected 2329725800U 160: file acs1996_2.png gave hash 910959002U not the expected 2996350718U 160: file acs1996_3.svg gave hash 510450189U not the expected 879041204U 160: file acs1996_8.svg gave hash 3359655656U not the expected 4110469272U 160: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U -160: [05:51:26] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. +160: [15:23:27] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. 160: file bond_highlights_8.svg gave hash 197391689U not the expected 3119784980U 160: file test_github5947.svg gave hash 737562322U not the expected 3122633523U -160: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U -160: file github6336_1.png gave hash 1930712448U not the expected 2958833204U -160: file AtropManyChiralsEnhanced.svg gave hash 643650995U not the expected 2256768013U 150: processing 150: launch :0 150: launch :1 150: launch :2 150: launch :3 +160: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U +160: file github6336_1.png gave hash 1930712448U not the expected 2958833204U +160: file AtropManyChiralsEnhanced.svg gave hash 643650995U not the expected 2256768013U 160: file testWedgingShouldBeOnSingleBond.svg gave hash 2637422009U not the expected 1002741488U 160: file testHighlightHeteroAtoms_1.svg gave hash 4006401146U not the expected 1769258632U 160: file testHighlightHeteroAtoms_2.svg gave hash 1248188292U not the expected 893937335U 160: file testGithub_7739_1.svg gave hash 1295207536U not the expected 2615562225U 160: file testGithub_7739_3.svg gave hash 3850267352U not the expected 1037942338U 160: file testGithub_7739_4.svg gave hash 1411616678U not the expected 3549083171U -160: [05:51:28] +160: [15:23:28] 160: 160: **** 160: Pre-condition Violation @@ -30564,20 +30595,20 @@ 160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x0000AAAAD0E75780 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x0000AAAAD0F4514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x0000AAAAD0F45B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x0000AAAAD0F45F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x0000AAAAD0F1A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x0000AAAAD0F1AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x0000AAAAD0E6EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x0000FFFFA3ED229C in /lib/aarch64-linux-gnu/libc.so.6 +160: 8# 0x0000AAAAE5965780 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x0000AAAAE5A3514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x0000AAAAE5A35B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x0000AAAAE5A35F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x0000AAAAE5A0A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x0000AAAAE5A0AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x0000AAAAE595EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x0000FFFF9F38229C in /lib/aarch64-linux-gnu/libc.so.6 160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -160: 17# 0x0000AAAAD0E6EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 17# 0x0000AAAAE595EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: ---------- 160: **** 160: -160: [05:51:28] +160: [15:23:28] 160: 160: **** 160: Range Error @@ -30594,20 +30625,20 @@ 160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x0000AAAAD0E751C4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x0000AAAAD0F4514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x0000AAAAD0F45B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x0000AAAAD0F45F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x0000AAAAD0F1A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x0000AAAAD0F1AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x0000AAAAD0E6EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x0000FFFFA3ED229C in /lib/aarch64-linux-gnu/libc.so.6 +160: 8# 0x0000AAAAE59651C4 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x0000AAAAE5A3514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x0000AAAAE5A35B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x0000AAAAE5A35F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x0000AAAAE5A0A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x0000AAAAE5A0AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x0000AAAAE595EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x0000FFFF9F38229C in /lib/aarch64-linux-gnu/libc.so.6 160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -160: 17# 0x0000AAAAD0E6EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 17# 0x0000AAAAE595EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: ---------- 160: **** 160: -160: [05:51:28] +160: [15:23:28] 160: 160: **** 160: Range Error @@ -30624,68 +30655,67 @@ 160: 5# RDKit::MolDraw2D_detail::DrawMol::extractAll(double) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 6# RDKit::MolDraw2D_detail::DrawMol::createDrawObjects() in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 160: 7# RDKit::MolDraw2D::drawMoleculeWithHighlights(RDKit::ROMol const&, std::__cxx11::basic_string, std::allocator > const&, std::map >, std::less, std::allocator > > > > const&, std::map >, std::less, std::allocator > > > > const&, std::map, std::allocator > > const&, std::map, std::allocator > > const&, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitMolDraw2D.so.1 -160: 8# 0x0000AAAAD0E7582C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 9# 0x0000AAAAD0F4514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 10# 0x0000AAAAD0F45B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 11# 0x0000AAAAD0F45F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 12# 0x0000AAAAD0F1A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 13# 0x0000AAAAD0F1AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 14# 0x0000AAAAD0E6EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -160: 15# 0x0000FFFFA3ED229C in /lib/aarch64-linux-gnu/libc.so.6 +160: 8# 0x0000AAAAE596582C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 9# 0x0000AAAAE5A3514C in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 10# 0x0000AAAAE5A35B00 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 11# 0x0000AAAAE5A35F34 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 12# 0x0000AAAAE5A0A7F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 13# 0x0000AAAAE5A0AD44 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 14# 0x0000AAAAE595EA70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 15# 0x0000FFFF9F38229C in /lib/aarch64-linux-gnu/libc.so.6 160: 16# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -160: 17# 0x0000AAAAD0E6EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +160: 17# 0x0000AAAAE595EB30 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 160: ---------- 160: **** 160: 160: file testSmallReactionCanvas.svg gave hash 3859901121U not the expected 2238356155U +163: [15:23:28] The provided InitialSeed is not an MCS and will be ignored 160: =============================================================================== 160: All tests passed (6853 assertions in 115 test cases) 160: -158/235 Test #160: moldraw2DTestCatch ..................... Passed 5.53 sec +158/235 Test #160: moldraw2DTestCatch ..................... Passed 4.45 sec test 170 Start 170: testRascalMCES 170: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 170: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 170: Test timeout computed to be: 1500 -163: [05:51:29] The provided InitialSeed is not an MCS and will be ignored 169: ......... 169: ---------------------------------------------------------------------- -169: Ran 9 tests in 2.222s +169: Ran 9 tests in 2.908s 169: 169: OK -164: ........................................[05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: [05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: [05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: .[05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: [05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: [05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: .[05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: [05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: [05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: .[05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: [05:51:29] The provided InitialSeed is not an MCS and will be ignored -164: [05:51:29] The provided InitialSeed is not an MCS and will be ignored -159/235 Test #169: pyMMPA ................................. Passed 2.85 sec +159/235 Test #169: pyMMPA ................................. Passed 3.54 sec test 171 Start 171: testRascalCluster 171: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 171: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 171: Test timeout computed to be: 1500 +164: ........................................[15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: .[15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: .[15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: .[15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored +164: [15:23:30] The provided InitialSeed is not an MCS and will be ignored 164: ................. 164: ---------------------------------------------------------------------- -164: Ran 60 tests in 4.713s +164: Ran 60 tests in 5.227s 164: 164: OK -160/235 Test #164: pyFMCS ................................. Passed 5.39 sec +160/235 Test #164: pyFMCS ................................. Passed 5.79 sec test 172 Start 172: pyRascalMCES 172: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 172: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap 172: Test timeout computed to be: 1500 -172: ..........[05:51:29] Too many matching bond pairs (1032) so can't continue. 159: Done 159: ----------------- Test Github #781: Rendering single-atom molecules 159: Done @@ -30739,6 +30769,7 @@ 159: Done 159: ----------------- Testing drawMolecules 159: file test12_1.svg gave hash 76786371U not the expected 826649652U +172: ..........[15:23:32] Too many matching bond pairs (1032) so can't continue. 159: Done 159: ----------------- Test JSON Configuration 159: Done @@ -30809,7 +30840,7 @@ 159: Done 159: ----------------- Test AND queries 159: Done -161/235 Test #159: moldraw2DTest1 ......................... Passed 9.57 sec +161/235 Test #159: moldraw2DTest1 ......................... Passed 8.98 sec test 173 Start 173: testSynthonSpaceSubstructureSearch @@ -30818,29 +30849,31 @@ 173: Test timeout computed to be: 1500 172: .... 172: ---------------------------------------------------------------------- -172: Ran 14 tests in 2.099s +172: Ran 14 tests in 2.663s 172: 172: OK -162/235 Test #172: pyRascalMCES ........................... Passed 2.64 sec +162/235 Test #172: pyRascalMCES ........................... Passed 3.42 sec test 174 Start 174: testCIPLabeler 174: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 174: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler 174: Test timeout computed to be: 1500 -174: Randomness seeded to: 1701089859 -174: [05:51:32] non kekulizable aromatic bond being treated as bond order 1 -174: [05:51:32] non kekulizable aromatic bond being treated as bond order 1 -174: [05:51:32] non kekulizable aromatic bond being treated as bond order 1 -174: [05:51:32] non kekulizable aromatic bond being treated as bond order 1 -174: [05:51:32] non kekulizable aromatic bond being treated as bond order 1 -174: [05:51:32] non kekulizable aromatic bond being treated as bond order 1 -174: [05:51:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored -174: [05:51:32] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +173: Randomness seeded to: 2728322522 +173: [15:23:34] Writing the enumerated file may take quite some time and result in a large file. +174: Randomness seeded to: 4074356387 +174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 +174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 +174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 +174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 +174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 +174: [15:23:34] non kekulizable aromatic bond being treated as bond order 1 +174: [15:23:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored +174: [15:23:35] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 7 ignored 174: =============================================================================== 174: All tests passed (6577 assertions in 19 test cases) 174: -163/235 Test #174: testCIPLabeler ......................... Passed 0.38 sec +163/235 Test #174: testCIPLabeler ......................... Passed 0.36 sec test 175 Start 175: pyCIPLabelsWrapTest @@ -30849,55 +30882,55 @@ 175: Test timeout computed to be: 1500 175: .... 175: ---------------------------------------------------------------------- -175: Ran 4 tests in 0.026s +175: Ran 4 tests in 0.052s 175: 175: OK -173: Randomness seeded to: 725004711 -173: [05:51:33] Writing the enumerated file may take quite some time and result in a large file. -164/235 Test #175: pyCIPLabelsWrapTest .................... Passed 0.68 sec +164/235 Test #175: pyCIPLabelsWrapTest .................... Passed 0.81 sec test 176 Start 176: pyCIPLabelsValidation 176: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 176: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 176: Test timeout computed to be: 1500 -152: .............[05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:34] Molecule does not have explicit Hs. Consider calling AddHs() -171: Randomness seeded to: 860426402 +152: .............[15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:37] Molecule does not have explicit Hs. Consider calling AddHs() +171: Randomness seeded to: 570871552 171: /build/reproducible-path/rdkit-202409.6/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -173: [05:51:37] Building the fingerprints may take some time. -152: ...[05:51:37] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:37] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:37] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:37] Molecule does not have explicit Hs. Consider calling AddHs() -152: [05:51:37] Molecule does not have explicit Hs. Consider calling AddHs() +170: Randomness seeded to: 1355402787 +170: [15:23:39] Timed out after 11 seconds. +173: [15:23:40] Building the fingerprints may take some time. +152: ...[15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() +152: [15:23:41] Molecule does not have explicit Hs. Consider calling AddHs() 152: ... 152: ---------------------------------------------------------------------- -152: Ran 19 tests in 16.378s +152: Ran 19 tests in 17.678s 152: 152: OK 152: Testing MolAlign Wrappers -165/235 Test #152: pyMolAlign ............................. Passed 16.91 sec +165/235 Test #152: pyMolAlign ............................. Passed 18.28 sec test 177 Start 177: deprotectTest 177: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 177: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect 177: Test timeout computed to be: 1500 -177: Randomness seeded to: 2590223766 +177: Randomness seeded to: 1799758318 177: =============================================================================== 177: All tests passed (111 assertions in 3 test cases) 177: -166/235 Test #177: deprotectTest .......................... Passed 0.12 sec +166/235 Test #177: deprotectTest .......................... Passed 0.22 sec test 178 Start 178: pyDeprotect @@ -30906,7 +30939,7 @@ 178: Test timeout computed to be: 1500 178: ..... 178: ---------------------------------------------------------------------- -178: Ran 5 tests in 0.068s +178: Ran 5 tests in 0.163s 178: 178: OK 178: Testing tert-butyldimethylsilyl @@ -30959,7 +30992,7 @@ 178: Testing acetamide 178: Testing carbobenzyloxy 178: Testing Acetal/Ketal -167/235 Test #178: pyDeprotect ............................ Passed 0.80 sec +167/235 Test #178: pyDeprotect ............................ Passed 1.94 sec test 179 Start 179: testReducedGraphs @@ -30984,57 +31017,55 @@ 179: 179: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 179: -168/235 Test #179: testReducedGraphs ...................... Passed 0.06 sec +168/235 Test #179: testReducedGraphs ...................... Passed 0.17 sec test 180 Start 180: pyReducedGraphs 180: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 180: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap 180: Test timeout computed to be: 1500 -170: Randomness seeded to: 2657822070 -170: [05:51:39] Timed out after 11 seconds. 180: ..... 180: ---------------------------------------------------------------------- -180: Ran 5 tests in 0.041s +180: Ran 5 tests in 0.059s 180: 180: OK -169/235 Test #180: pyReducedGraphs ........................ Passed 0.66 sec +169/235 Test #180: pyReducedGraphs ........................ Passed 1.77 sec test 181 Start 181: trajectoryTest 181: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 181: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory 181: Test timeout computed to be: 1500 -170/235 Test #181: trajectoryTest ......................... Passed 0.52 sec +170/235 Test #181: trajectoryTest ......................... Passed 1.02 sec test 182 Start 182: substructLibraryTest 182: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 182: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 182: Test timeout computed to be: 1500 -182: [05:51:40] ------------------------------------- -182: [05:51:40] Test1 -182: [05:51:40] done -182: [05:51:40] ------------------------------------- -182: [05:51:40] Test2 -182: [05:51:41] done -182: [05:51:41] ------------------------------------- -182: [05:51:41] Test3 (stereo options) -182: [05:51:41] Done (stereo options) -182: [05:51:41] ------------------------------------- -182: [05:51:41] Test4 (trusted smiles) -182: [05:51:41] Done (trusted smiles) -182: [05:51:41] ------------------------------------- -182: [05:51:41] Testing C++ docs -182: [05:51:41] Done (C++ doc tests) -182: [05:51:41] ------------------------------------- -182: [05:51:41] Testing C++ ring query: PatternHolder -182: [05:51:41] Done (C++ ring query tests) -182: [05:51:41] ------------------------------------- -182: [05:51:41] Testing C++ ring query: TautomerPatternHolder -182: [05:51:41] Done (C++ ring query tests) -182: [05:51:41] ------------------------------------- -182: [05:51:41] Add Patterns +182: [15:23:46] ------------------------------------- +182: [15:23:46] Test1 +182: [15:23:47] done +182: [15:23:47] ------------------------------------- +182: [15:23:47] Test2 +182: [15:23:47] done +182: [15:23:47] ------------------------------------- +182: [15:23:47] Test3 (stereo options) +182: [15:23:48] Done (stereo options) +182: [15:23:48] ------------------------------------- +182: [15:23:48] Test4 (trusted smiles) +182: [15:23:48] Done (trusted smiles) +182: [15:23:48] ------------------------------------- +182: [15:23:48] Testing C++ docs +182: [15:23:48] Done (C++ doc tests) +182: [15:23:48] ------------------------------------- +182: [15:23:48] Testing C++ ring query: PatternHolder +182: [15:23:48] Done (C++ ring query tests) +182: [15:23:48] ------------------------------------- +182: [15:23:48] Testing C++ ring query: TautomerPatternHolder +182: [15:23:48] Done (C++ ring query tests) +182: [15:23:48] ------------------------------------- +182: [15:23:48] Add Patterns 176: VS001: PASSED 176: VS002: PASSED 176: VS003: PASSED @@ -31337,1184 +31368,1185 @@ 176: VS300: PASSED 176: Check finished: 0 molecules failed. 176: Failed: -148: .........[05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: .[05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -148: [05:51:42] Molecule does not have explicit Hs. Consider calling AddHs() -171/235 Test #176: pyCIPLabelsValidation .................. Passed 9.25 sec +171/235 Test #176: pyCIPLabelsValidation .................. Passed 15.53 sec test 183 Start 183: substructLibraryCatchTest 183: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 183: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 183: Test timeout computed to be: 1500 -183: Randomness seeded to: 1271746935 +183: Randomness seeded to: 112852166 183: =============================================================================== 183: All tests passed (171 assertions in 5 test cases) 183: -172/235 Test #183: substructLibraryCatchTest .............. Passed 1.84 sec +172/235 Test #183: substructLibraryCatchTest .............. Passed 1.79 sec test 184 Start 184: pySubstructLibrary 184: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 184: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 184: Test timeout computed to be: 1500 +150: --------------------------------- +150: test O3A multithreading bug +150: +150: --------------------------------- +150: testCrippenO3A multithreading +150: +150: generating reference data +182: [15:23:56] ------------------------------------- +182: [15:23:56] testing PatternHolder +182: [15:23:56] ------------------------------------- +182: [15:23:56] testing TautomerPatternHolder +182: [15:23:56] ------------------------------------- +182: [15:23:56] testSegFaultInHolder +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] [15:23:56] SMILES Parse Error: check for mistakes around position 1:SMILES Parse Error: SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: syntax error while parsing: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] [15:23:56] SMILES Parse Error: check for mistakes around position SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] SMILES Parse Error: syntax error while parsing: dsafsdf +182: [15:23:56] SMILES Parse Error: check for mistakes around position 1: +182: [15:23:56] dsafsdf +182: [15:23:56] ^ +182: [15:23:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +182: [15:23:56] ------------------------------------- +182: [15:23:56] Results do not depend on numThreads +150: processing +150: launch :0 +150: launch :1 +150: launch :2 +150: launch :3 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 163: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 163: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -163: TOTAL Time elapsed 23.01 seconds -173/235 Test #163: testFMCS ............................... Passed 23.08 sec +163: TOTAL Time elapsed 32.64 seconds +173/235 Test #163: testFMCS ............................... Passed 32.83 sec test 185 Start 185: testRGroupDecomp 185: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 185: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 185: Test timeout computed to be: 1500 -185: [05:51:47] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -185: [05:51:47] WARNING: not removing hydrogen atom with dummy atom neighbors -182: [05:51:47] ------------------------------------- -182: [05:51:47] testing PatternHolder -182: [05:51:47] ------------------------------------- -182: [05:51:47] testing TautomerPatternHolder 173: Query 0 -182: [05:51:47] ------------------------------------- -182: [05:51:47] testSegFaultInHolder -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position [05:51:47] 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] [05:51:47] SMILES Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: SMILES Parse Error: syntax error while parsing: [05:51:47] [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1:[05:51:47] -182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] [05:51:47] SMILES Parse Error: [05:51:47] SMILES Parse Error: syntax errorsyntax errorSMILES Parse Error: syntax error while parsing: while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf[05:51:47] dsafsdf -182: [05:51:47] while parsing: dsafsdf -182: -182: SMILES Parse Error: check for mistakes around position 1[05:51:47] [05:51:47] SMILES Parse Error: check for mistakes around position 1SMILES Parse Error: syntax error while parsing: : -182: dsafsdf: -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1:[05:51:47] dsafsdf -182: -182: [05:51:47] dsafsdf -182: SMILES Parse Error: check for mistakes around position [05:51:47] SMILES Parse Error: [05:51:47] ^[05:51:47] -182: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'1: -182: for input: '[05:51:47] dsafsdfdsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] [05:51:47] -182: dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: ^ -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[05:51:47] -182: SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: -182: SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:47] SMILES Parse Error: syntax error while parsing: dsafsdf -182: [05:51:47] SMILES Parse Error: check for mistakes around position 1: -182: [05:51:47] dsafsdf -182: [05:51:47] ^ -182: [05:51:47] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -182: [05:51:48] ------------------------------------- -182: [05:51:48] Results do not depend on numThreads -150: --------------------------------- -150: test O3A multithreading bug -150: -150: --------------------------------- -150: testCrippenO3A multithreading -150: -150: generating reference data -148: ... -148: ---------------------------------------------------------------------- -148: Ran 22 tests in 29.231s -148: -148: OK -174/235 Test #148: pyDistGeomHelpers ...................... Passed 29.94 sec +185: [15:23:58] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +185: [15:23:58] WARNING: not removing hydrogen atom with dummy atom neighbors +148: .........[15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: .[15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +148: [15:24:02] Molecule does not have explicit Hs. Consider calling AddHs() +185: iterative +185: bulk +185: bulk, no symmetry +182: [15:24:05] ------------------------------------- +182: [15:24:05] Results do not depend on numThreads (all same) +182: [15:24:06] ------------------------------------- +182: [15:24:06] testTautomerQueries +182: [15:24:06] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +182: [15:24:06] ------------------------------------- +182: [15:24:06] github3881 recursive smarts with rings +174/235 Test #182: substructLibraryTest ................... Passed 19.80 sec test 186 Start 186: testRGroupDecompInternals 186: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 186: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 186: Test timeout computed to be: 1500 -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -186: [05:51:48] WARNING: not removing hydrogen atom with dummy atom neighbors -175/235 Test #186: testRGroupDecompInternals .............. Passed 0.06 sec +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +186: [15:24:06] WARNING: not removing hydrogen atom with dummy atom neighbors +175/235 Test #186: testRGroupDecompInternals .............. Passed 0.22 sec test 187 Start 187: rgroupCatchTests 187: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 187: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 187: Test timeout computed to be: 1500 -150: processing -150: launch :0 -150: launch :1 -150: launch :2 -150: launch :3 -187: Randomness seeded to: 2312010200 +185: [15:24:07] Relabelling existing label +187: Randomness seeded to: 1985732401 187: =============================================================================== 187: All tests passed (1475 assertions in 14 test cases) 187: -176/235 Test #187: rgroupCatchTests ....................... Passed 0.50 sec +176/235 Test #187: rgroupCatchTests ....................... Passed 1.34 sec test 188 Start 188: pyRGroupDecomposition 188: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 188: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 188: Test timeout computed to be: 1500 -185: iterative -185: bulk -188: .................... -188: ---------------------------------------------------------------------- -188: Ran 20 tests in 2.207s -188: -188: OK -177/235 Test #188: pyRGroupDecomposition .................. Passed 2.95 sec +185: Best mapping +173: Query 1 +177/235 Test #185: testRGroupDecomp ....................... Passed 10.58 sec test 189 Start 189: molInterchangeTest1 189: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 189: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 189: Test timeout computed to be: 1500 -189: [05:51:52] test1: basics -189: [05:51:52] done -189: [05:51:52] test2: basic writing +189: [15:24:08] test1: basics +189: [15:24:08] done +189: [15:24:08] test2: basic writing 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,0]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} -189: [05:51:52] done -189: [05:51:52] test3: writing conformers +189: [15:24:08] done +189: [15:24:08] test3: writing conformers 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1988,-0.0452],[-0.3332,0.4556],[0.166,1.322],[0.5332,-0.0438],[-2.0652,0.4542],[-0.834,1.3212]]},{"dim":3,"coords":[[0.9554,-0.3743,-0.4679],[-0.3616,-0.1311,-0.0795],[-0.5097,1.6256,0.1706],[-0.5779,-0.792,1.1042],[1.5277,0.1064,0.1628],[-1.0339,-0.4346,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.6","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -189: [05:51:52] done -189: [05:51:52] test4: writing properties +189: [15:24:08] done +189: [15:24:08] test4: writing properties 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,0]}]}]} -189: [05:51:52] done -189: [05:51:52] test5: writing partial charges +189: [15:24:08] done +189: [15:24:08] test5: writing partial charges 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2024.09.6","values":[0.5,-0.5]}]}]} -189: [05:51:52] testing parse options -189: [05:51:52] done -189: [05:51:52] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +189: [15:24:08] testing parse options +189: [15:24:08] done +189: [15:24:08] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 189: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2024.09.6","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -189: [05:51:52] done -189: [05:51:52] testing 'either' stereochemistry -189: [05:51:52] done -178/235 Test #189: molInterchangeTest1 .................... Passed 0.07 sec +189: [15:24:08] done +189: [15:24:08] testing 'either' stereochemistry +189: [15:24:08] done +178/235 Test #189: molInterchangeTest1 .................... Passed 0.14 sec test 190 Start 190: molInterchangeCatchTest 190: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 190: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 190: Test timeout computed to be: 1500 -190: Randomness seeded to: 1203915703 -190: [05:51:52] unrecognized bond type 12 set to zero while writing -190: [05:51:52] unrecognized bond type 0 set to zero while writing +190: Randomness seeded to: 3774299301 +190: [15:24:08] unrecognized bond type 12 set to zero while writing +190: [15:24:08] unrecognized bond type 0 set to zero while writing 190: =============================================================================== 190: All tests passed (125 assertions in 7 test cases) 190: -179/235 Test #190: molInterchangeCatchTest ................ Passed 0.07 sec +179/235 Test #190: molInterchangeCatchTest ................ Passed 0.06 sec test 191 Start 191: pyMolInterchange @@ -32523,11 +32555,10 @@ 191: Test timeout computed to be: 1500 191: .. 191: ---------------------------------------------------------------------- -191: Ran 2 tests in 0.016s +191: Ran 2 tests in 0.019s 191: 191: OK -185: bulk, no symmetry -180/235 Test #191: pyMolInterchange ....................... Passed 0.61 sec +180/235 Test #191: pyMolInterchange ....................... Passed 0.65 sec test 192 Start 192: testSLNParse @@ -32547,36 +32578,38 @@ 192: 2 0->3 order: 1 192: 3 0->4 order: 1 192: 4 0->5 order: 1 -192: [05:51:52] SLN Parse Error: syntax error while parsing: CH4[I=13] -192: [05:51:52] Failed parsing SLN 'CH4[I=13]' -192: [05:51:52] SLN Parser error: Atom ID 1 appears *after* its ring closure. -192: [05:51:52] SLN Parser error: Ring closure 1 does not have a corresponding opener. -192: [05:51:52] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -192: [05:51:52] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -192: [05:51:52] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -192: [05:51:52] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -192: [05:51:52] SLN Parse Error: syntax error while parsing: CH4 fff -192: [05:51:52] Failed parsing SLN 'CH4 fff' -192: [05:51:52] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -192: [05:51:52] Failed parsing SLN 'C[charge=+1] foo' -192: [05:51:52] Query property 'is' ignored on non-query atom -192: [05:51:52] Query property 'is' ignored on non-query atom -181/235 Test #192: testSLNParse ........................... Passed 0.04 sec +192: [15:24:09] SLN Parse Error: syntax error while parsing: CH4[I=13] +192: [15:24:09] Failed parsing SLN 'CH4[I=13]' +192: [15:24:09] SLN Parser error: Atom ID 1 appears *after* its ring closure. +192: [15:24:09] SLN Parser error: Ring closure 1 does not have a corresponding opener. +192: [15:24:09] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +192: [15:24:09] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +192: [15:24:09] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +192: [15:24:09] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +192: [15:24:09] SLN Parse Error: syntax error while parsing: CH4 fff +192: [15:24:09] Failed parsing SLN 'CH4 fff' +192: [15:24:09] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +192: [15:24:09] Failed parsing SLN 'C[charge=+1] foo' +192: [15:24:09] Query property 'is' ignored on non-query atom +192: [15:24:09] Query property 'is' ignored on non-query atom +181/235 Test #192: testSLNParse ........................... Passed 0.25 sec test 193 Start 193: pySLNParse 193: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/SLNParse/Wrap/testSLN.py" 193: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 193: Test timeout computed to be: 1500 -182: [05:51:52] ------------------------------------- -182: [05:51:52] Results do not depend on numThreads (all same) -185: [05:51:53] Relabelling existing label -182: [05:51:53] ------------------------------------- -182: [05:51:53] testTautomerQueries -182: [05:51:53] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -182: [05:51:53] ------------------------------------- -182: [05:51:53] github3881 recursive smarts with rings -182/235 Test #182: substructLibraryTest ................... Passed 12.93 sec +148: ... +148: ---------------------------------------------------------------------- +148: Ran 22 tests in 48.637s +148: +148: OK +188: .................... +188: ---------------------------------------------------------------------- +188: Ran 20 tests in 1.307s +188: +188: OK +182/235 Test #188: pyRGroupDecomposition .................. Passed 2.29 sec test 194 Start 194: pyGraphMolWrap @@ -32585,18 +32618,17 @@ 194: Test timeout computed to be: 1500 193: .. 193: ---------------------------------------------------------------------- -193: Ran 2 tests in 0.014s +193: Ran 2 tests in 0.018s 193: 193: OK -185: Best mapping -183/235 Test #193: pySLNParse ............................. Passed 0.66 sec +183/235 Test #148: pyDistGeomHelpers ...................... Passed 49.82 sec test 195 Start 195: pyTestConformerWrap 195: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testConformer.py" 195: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 195: Test timeout computed to be: 1500 -184/235 Test #185: testRGroupDecomp ....................... Passed 6.30 sec +184/235 Test #193: pySLNParse ............................. Passed 0.89 sec test 196 Start 196: pyTestTrajectory @@ -32605,34 +32637,43 @@ 196: Test timeout computed to be: 1500 195: ...... 195: ---------------------------------------------------------------------- -195: Ran 6 tests in 0.017s +195: Ran 6 tests in 0.057s 195: 195: OK -194: ..............[05:51:53] SMARTS Parse Error: syntax error while parsing: fiib -194: [05:51:53] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -194: ....[05:51:53] ERROR: Problems encountered parsing data fields -194: [05:51:53] ERROR: moving to the beginning of the next molecule -194: [05:51:53] ERROR: Problems encountered parsing data fields -194: [05:51:53] ERROR: moving to the beginning of the next molecule -194: [05:51:53] Spurious data before the first property will be ignored -194: [05:51:53] Property will be truncated after the first blank line -194: [05:51:53] Property will be truncated after the first blank line -194: [05:51:53] Property will be truncated after the first blank line -194: [05:51:53] ERROR: Problems encountered parsing data fields -194: [05:51:53] ERROR: moving to the beginning of the next molecule -194: [05:51:53] ERROR: Problems encountered parsing data fields -194: [05:51:53] ERROR: moving to the beginning of the next molecule -194: [05:51:53] Spurious data before the first property will be ignored -194: [05:51:53] Property will be truncated after the first blank line -194: [05:51:53] Property will be truncated after the first blank line -194: [05:51:53] Property will be truncated after the first blank line -194: [05:51:53] ERROR: Problems encountered parsing data fields -194: [05:51:53] ERROR: moving to the beginning of the next molecule -194: [05:51:53] Property will be truncated after the first blank line -194: [05:51:53] ERROR: Problems encountered parsing data fields -194: [05:51:53] ERROR: moving to the beginning of the next molecule -194: [05:51:53] Property will be truncated after the first blank line -196: [05:51:53] +194: ..............[15:24:11] SMARTS Parse Error: syntax error while parsing: fiib +194: [15:24:11] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +194: ....[15:24:11] ERROR: Problems encountered parsing data fields +194: [15:24:11] ERROR: moving to the beginning of the next molecule +194: [15:24:11] ERROR: Problems encountered parsing data fields +194: [15:24:11] ERROR: moving to the beginning of the next molecule +194: [15:24:11] Spurious data before the first property will be ignored +194: [15:24:11] Property will be truncated after the first blank line +194: [15:24:11] Property will be truncated after the first blank line +194: [15:24:11] Property will be truncated after the first blank line +194: [15:24:11] ERROR: Problems encountered parsing data fields +194: [15:24:11] ERROR: moving to the beginning of the next molecule +194: [15:24:11] ERROR: Problems encountered parsing data fields +194: [15:24:11] ERROR: moving to the beginning of the next molecule +194: [15:24:11] Spurious data before the first property will be ignored +194: [15:24:11] Property will be truncated after the first blank line +194: [15:24:11] Property will be truncated after the first blank line +194: [15:24:11] Property will be truncated after the first blank line +194: [15:24:11] ERROR: Problems encountered parsing data fields +194: [15:24:11] ERROR: moving to the beginning of the next molecule +194: [15:24:11] Property will be truncated after the first blank line +194: [15:24:11] ERROR: Problems encountered parsing data fields +194: [15:24:11] ERROR: moving to the beginning of the next molecule +194: [15:24:11] Property will be truncated after the first blank line +194: .[15:24:11] SMILES Parse Error: syntax error while parsing: fail +194: [15:24:11] SMILES Parse Error: check for mistakes around position 1: +194: [15:24:11] fail +194: [15:24:11] ^ +194: [15:24:11] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +194: [15:24:11] ERROR: Smiles parse error on line 2 +194: [15:24:11] ERROR: Cannot create molecule from : 'fail' +194: >>> This may result in an infinite loop. It should finish almost instantly +194: <<< OK, it finished. +196: [15:24:11] 196: 196: **** 196: Pre-condition Violation @@ -32646,23 +32687,23 @@ 196: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -32694,13 +32735,13 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[05:51:53] +196: .[15:24:11] 196: 196: **** 196: Pre-condition Violation @@ -32714,23 +32755,23 @@ 196: 2# RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -32762,37 +32803,28 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -194: .[05:51:53] SMILES Parse Error: syntax error while parsing: fail -194: [05:51:53] SMILES Parse Error: check for mistakes around position 1: -194: [05:51:53] fail -194: [05:51:53] ^ -194: [05:51:53] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -194: [05:51:53] ERROR: Smiles parse error on line 2 -194: [05:51:53] ERROR: Cannot create molecule from : 'fail' -194: >>> This may result in an infinite loop. It should finish almost instantly -194: <<< OK, it finished. -194: ............[05:51:53] Explicit valence for atom # 1 C, 5, is greater than permitted -194: ......[05:51:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -194: [05:51:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -194: [05:51:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -185/235 Test #195: pyTestConformerWrap .................... Passed 0.52 sec +194: ............[15:24:11] Explicit valence for atom # 1 C, 5, is greater than permitted +185/235 Test #195: pyTestConformerWrap .................... Passed 1.02 sec test 197 Start 197: pyTestSGroups 197: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testSGroups.py" 197: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 197: Test timeout computed to be: 1500 -194: [05:51:53] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: ......[15:24:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: [15:24:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: [15:24:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: [15:24:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 194: .inWedges: [H]C12C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H] |(-0.612,-0.6446,0.635;0.0021,-0.0041,0.002;-0.0187,1.5258,0.0104;-0.6498,2.1424,0.6504;1.5111,1.5466,-0.0041;2.1372,2.1804,0.624;1.5319,0.0168,-0.0125;2.175,-0.6067,0.6086;1.5173,0.025,-1.5424;2.1484,-0.5936,-2.1805;-0.0125,0.0041,-1.5279;-0.6405,-0.6297,-2.154;-0.0333,1.534,-1.5195;-0.6783,2.1574,-2.1387;1.4965,1.5548,-1.534;2.1106,2.1972,-2.1651)| -194: ........[05:51:53] non-ring atom 0 marked aromatic -194: [05:51:53] non-ring atom 0 marked aromatic -194: [05:51:53] +194: ........[15:24:11] non-ring atom 0 marked aromatic +194: [15:24:11] non-ring atom 0 marked aromatic +194: [15:24:11] 194: 194: **** 194: Range Error @@ -32805,9 +32837,9 @@ 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -194: 4# 0x0000FFFFB0C66C70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 4# 0x0000FFFFB73A6C70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 6# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 6# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32818,17 +32850,17 @@ 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 21# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 21# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 27# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 27# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 28# _PyObject_MakeTpCall in /usr/bin/python3 194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 30# 0x00000000005335D0 in /usr/bin/python3 @@ -32860,15 +32892,15 @@ 194: 56# 0x0000000000627010 in /usr/bin/python3 194: 57# Py_RunMain in /usr/bin/python3 194: 58# Py_BytesMain in /usr/bin/python3 -194: 59# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 59# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 61# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [05:51:53] non-ring atom 0 marked aromatic -194: [05:51:53] non-ring atom 0 marked aromatic -194: [05:51:53] +194: [15:24:11] non-ring atom 0 marked aromatic +194: [15:24:11] non-ring atom 0 marked aromatic +194: [15:24:11] 194: 194: **** 194: Range Error @@ -32881,9 +32913,9 @@ 194: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -194: 4# 0x0000FFFFB0C66C70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 4# 0x0000FFFFB73A6C70 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 6# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 6# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -32894,17 +32926,17 @@ 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 21# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 21# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 27# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 27# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 28# _PyObject_MakeTpCall in /usr/bin/python3 194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 30# 0x00000000005335D0 in /usr/bin/python3 @@ -32936,15 +32968,15 @@ 194: 56# 0x0000000000627010 in /usr/bin/python3 194: 57# Py_RunMain in /usr/bin/python3 194: 58# Py_BytesMain in /usr/bin/python3 -194: 59# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 59# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 61# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: ...............[05:51:54] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -194: [05:51:54] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -196: .[05:51:54] +194: ...............[15:24:11] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +194: [15:24:11] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +196: .[15:24:11] 196: 196: **** 196: Range Error @@ -32959,23 +32991,23 @@ 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 22# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 22# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005335D0 in /usr/bin/python3 @@ -33007,13 +33039,13 @@ 196: 51# 0x0000000000627010 in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 -196: 54# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 54# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[05:51:54] +196: .[15:24:11] 196: 196: **** 196: Pre-condition Violation @@ -33027,23 +33059,23 @@ 196: 2# RDKit::readAmberTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -33075,13 +33107,13 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: ..[05:51:54] +196: ..[15:24:11] 196: 196: **** 196: Pre-condition Violation @@ -33095,23 +33127,23 @@ 196: 2# RDKit::readGromosTrajectory(std::__cxx11::basic_string, std::allocator > const&, RDKit::Trajectory&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl, std::allocator > const&, RDKit::Trajectory&), boost::python::default_call_policies, boost::mpl::vector3, std::allocator > const&, RDKit::Trajectory&> > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -33143,13 +33175,13 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[05:51:54] +196: .[15:24:11] 196: 196: **** 196: Pre-condition Violation @@ -33163,23 +33195,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -33211,13 +33243,13 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [05:51:54] +196: [15:24:11] 196: 196: **** 196: Pre-condition Violation @@ -33231,23 +33263,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -33279,13 +33311,13 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[05:51:54] +196: .[15:24:11] 196: 196: **** 196: Range Error @@ -33300,23 +33332,23 @@ 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 22# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 22# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005335D0 in /usr/bin/python3 @@ -33348,13 +33380,13 @@ 196: 51# 0x0000000000627010 in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 -196: 54# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 54# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [05:51:54] +196: [15:24:11] 196: 196: **** 196: Range Error @@ -33368,23 +33400,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -33416,13 +33448,13 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: .[05:51:54] +196: .[15:24:11] 196: 196: **** 196: Range Error @@ -33437,23 +33469,23 @@ 196: 3# RDKit::getSnapshot_wrap(RDKit::Trajectory*, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::caller_py_function_impl, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 6# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 6# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 16# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 16# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 21# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 22# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 22# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 23# _PyObject_MakeTpCall in /usr/bin/python3 196: 24# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 25# 0x00000000005335D0 in /usr/bin/python3 @@ -33485,13 +33517,13 @@ 196: 51# 0x0000000000627010 in /usr/bin/python3 196: 52# Py_RunMain in /usr/bin/python3 196: 53# Py_BytesMain in /usr/bin/python3 -196: 54# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 54# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 55# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 56# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [05:51:54] +196: [15:24:11] 196: 196: **** 196: Pre-condition Violation @@ -33505,23 +33537,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -33553,13 +33585,13 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- 196: **** 196: -196: [05:51:54] +196: [15:24:11] 196: 196: **** 196: Pre-condition Violation @@ -33573,23 +33605,23 @@ 196: 2# RDKit::Snapshot::getPoint2D(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitTrajectory.so.1 196: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdtrajectory.so 196: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 5# 0x0000FFFFB9772680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 5# 0x0000FFFFBD6C2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 196: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 196: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 11# 0x0000FFFFB7D4B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 12# 0x0000FFFFB7D4B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 13# 0x0000FFFFB7D4B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 14# 0x0000FFFFB7D4B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -196: 15# 0x0000FFFFB7D4B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 11# 0x0000FFFFBBC9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 12# 0x0000FFFFBBC9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 13# 0x0000FFFFBBC9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 14# 0x0000FFFFBBC9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +196: 15# 0x0000FFFFBBC9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 196: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 196: 20# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -196: 21# 0x0000FFFFB976F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +196: 21# 0x0000FFFFBD6BF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 196: 22# _PyObject_MakeTpCall in /usr/bin/python3 196: 23# _PyEval_EvalFrameDefault in /usr/bin/python3 196: 24# 0x00000000005335D0 in /usr/bin/python3 @@ -33621,7 +33653,7 @@ 196: 50# 0x0000000000627010 in /usr/bin/python3 196: 51# Py_RunMain in /usr/bin/python3 196: 52# Py_BytesMain in /usr/bin/python3 -196: 53# 0x0000FFFFB9F5229C in /lib/aarch64-linux-gnu/libc.so.6 +196: 53# 0x0000FFFFBDEA229C in /lib/aarch64-linux-gnu/libc.so.6 196: 54# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 196: 55# _start in /usr/bin/python3 196: ---------- @@ -33629,35 +33661,34 @@ 196: 196: . 196: ---------------------------------------------------------------------- -196: Ran 9 tests in 0.243s +196: Ran 9 tests in 0.426s 196: 196: OK 196: Testing Trajectory wrapper -194: ..............[05:51:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -194: [05:51:54] Explicit valence for atom # 1 C, 5, is greater than permitted -186/235 Test #196: pyTestTrajectory ....................... Passed 0.73 sec +194: ..............[15:24:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +194: [15:24:11] Explicit valence for atom # 1 C, 5, is greater than permitted +186/235 Test #196: pyTestTrajectory ....................... Passed 1.37 sec test 198 Start 198: pyTestThreads 198: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testThreads.py" 198: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 198: Test timeout computed to be: 1500 -173: Query 1 197: ............. 197: ---------------------------------------------------------------------- -197: Ran 13 tests in 0.042s +197: Ran 13 tests in 0.078s 197: 197: OK 197: Testing SubstanceGroups wrapper -187/235 Test #197: pyTestSGroups .......................... Passed 0.63 sec +187/235 Test #197: pyTestSGroups .......................... Passed 1.18 sec test 199 Start 199: pyTestMultithreadedMolSupplier 199: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 199: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 199: Test timeout computed to be: 1500 -194: ............................[05:51:54] unable to set wavy bonds for double bonds: 3 -194: .............[05:51:54] +194: ............................[15:24:13] unable to set wavy bonds for double bonds: 3 +194: .............[15:24:13] 194: 194: **** 194: Range Error @@ -33672,7 +33703,7 @@ 194: 3# RDKit::RWMol::removeAtom(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 6# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 6# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33683,17 +33714,17 @@ 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 21# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 21# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 26# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 27# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 27# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 28# _PyObject_MakeTpCall in /usr/bin/python3 194: 29# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 30# 0x00000000005335D0 in /usr/bin/python3 @@ -33725,7 +33756,7 @@ 194: 56# 0x0000000000627010 in /usr/bin/python3 194: 57# Py_RunMain in /usr/bin/python3 194: 58# Py_BytesMain in /usr/bin/python3 -194: 59# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 59# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 60# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 61# _start in /usr/bin/python3 194: ---------- @@ -33733,32 +33764,33 @@ 194: 199: .s. 199: ---------------------------------------------------------------------- -199: Ran 3 tests in 0.231s +199: Ran 3 tests in 0.137s 199: 199: OK (skipped=1) 199: Testing Smiles and SD MultithreadedMolSupplier -188/235 Test #199: pyTestMultithreadedMolSupplier ......... Passed 0.69 sec +188/235 Test #199: pyTestMultithreadedMolSupplier ......... Passed 1.12 sec test 200 Start 200: pyTestPropertyLists 200: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Wrap/testPropertyLists.py" 200: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 200: Test timeout computed to be: 1500 -200: [05:51:55] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -200: [05:51:55] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -200: [05:51:55] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -200: .[05:51:55] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -200: [05:51:55] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -200: [05:51:55] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -200: ...[05:51:55] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -200: [05:51:55] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -200: [05:51:55] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: Query 2 +200: [15:24:14] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +200: [15:24:14] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +200: [15:24:14] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +200: .[15:24:14] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +200: [15:24:14] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +200: [15:24:14] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +200: ...[15:24:14] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +200: [15:24:14] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +200: [15:24:14] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 200: . 200: ---------------------------------------------------------------------- -200: Ran 5 tests in 0.016s +200: Ran 5 tests in 0.037s 200: 200: OK -189/235 Test #200: pyTestPropertyLists .................... Passed 0.44 sec +189/235 Test #200: pyTestPropertyLists .................... Passed 0.93 sec test 201 Start 201: pyCDXMLTest @@ -33767,36 +33799,191 @@ 201: Test timeout computed to be: 1500 201: . 201: ---------------------------------------------------------------------- -201: Ran 1 test in 0.015s +201: Ran 1 test in 0.023s 201: 201: OK -190/235 Test #201: pyCDXMLTest ............................ Passed 0.52 sec +190/235 Test #201: pyCDXMLTest ............................ Passed 0.83 sec test 202 Start 202: molStandardizeTest 202: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 202: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 202: Test timeout computed to be: 1500 -194: ....................[05:51:56] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:51:56] Explicit valence for atom # 6 F, 2, is greater than permitted -194: [05:51:56] Can't kekulize mol. Unkekulized atoms: 3 4 5 -194: .................[05:51:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -191/235 Test #202: molStandardizeTest ..................... Passed 1.42 sec +194: ....................[15:24:16] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:16] Explicit valence for atom # 6 F, 2, is greater than permitted +194: [15:24:16] Can't kekulize mol. Unkekulized atoms: 3 4 5 +194: .................[15:24:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +184: ......[15:24:17] +184: +184: **** +184: Pre-condition Violation +184: RingInfo not initialized +184: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +184: Failed Expression: df_init +184: ---------- +184: Stacktrace: +184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +184: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +184: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 +184: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +184: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 12# 0x0000FFFF9118EB90 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 14# 0x0000FFFF92BF2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +184: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +184: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +184: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 20# 0x0000FFFF910EB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 21# 0x0000FFFF910EB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 22# 0x0000FFFF910EB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 23# 0x0000FFFF910EB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 24# 0x0000FFFF910EB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +184: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +184: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +184: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +184: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 30# 0x0000FFFF92BEF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 31# _PyObject_MakeTpCall in /usr/bin/python3 +184: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 33# 0x00000000005335D0 in /usr/bin/python3 +184: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 35# 0x00000000004AC3B4 in /usr/bin/python3 +184: 36# 0x0000000000665934 in /usr/bin/python3 +184: 37# _PyObject_MakeTpCall in /usr/bin/python3 +184: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 39# 0x00000000005335D0 in /usr/bin/python3 +184: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 41# 0x00000000004AC3B4 in /usr/bin/python3 +184: 42# 0x0000000000665934 in /usr/bin/python3 +184: 43# _PyObject_MakeTpCall in /usr/bin/python3 +184: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 45# 0x00000000005335D0 in /usr/bin/python3 +184: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 47# 0x00000000004AC3B4 in /usr/bin/python3 +184: 48# 0x0000000000665934 in /usr/bin/python3 +184: 49# _PyObject_MakeTpCall in /usr/bin/python3 +184: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 51# 0x0000000000505090 in /usr/bin/python3 +184: 52# _PyObject_MakeTpCall in /usr/bin/python3 +184: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 54# PyEval_EvalCode in /usr/bin/python3 +184: 55# 0x00000000005FFD24 in /usr/bin/python3 +184: 56# 0x00000000005F9904 in /usr/bin/python3 +184: 57# 0x0000000000627ED4 in /usr/bin/python3 +184: 58# 0x0000000000627274 in /usr/bin/python3 +184: 59# 0x0000000000627010 in /usr/bin/python3 +184: 60# Py_RunMain in /usr/bin/python3 +184: 61# Py_BytesMain in /usr/bin/python3 +184: 62# 0x0000FFFF935D229C in /lib/aarch64-linux-gnu/libc.so.6 +184: 63# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +184: 64# _start in /usr/bin/python3 +184: ---------- +184: **** +184: +184: [15:24:17] +184: +184: **** +184: Pre-condition Violation +184: RingInfo not initialized +184: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +184: Failed Expression: df_init +184: ---------- +184: Stacktrace: +184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 +184: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +184: 3# 0x0000FFFF90C42FA8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +184: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 +184: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 +184: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 13# 0x0000FFFF9118EB90 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 15# 0x0000FFFF92BF2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +184: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so +184: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so +184: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 21# 0x0000FFFF910EB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 22# 0x0000FFFF910EB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 23# 0x0000FFFF910EB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 24# 0x0000FFFF910EB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 25# 0x0000FFFF910EB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +184: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +184: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +184: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +184: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so +184: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 31# 0x0000FFFF92BEF25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +184: 32# _PyObject_MakeTpCall in /usr/bin/python3 +184: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 34# 0x00000000005335D0 in /usr/bin/python3 +184: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 36# 0x00000000004AC3B4 in /usr/bin/python3 +184: 37# 0x0000000000665934 in /usr/bin/python3 +184: 38# _PyObject_MakeTpCall in /usr/bin/python3 +184: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 40# 0x00000000005335D0 in /usr/bin/python3 +184: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 42# 0x00000000004AC3B4 in /usr/bin/python3 +184: 43# 0x0000000000665934 in /usr/bin/python3 +184: 44# _PyObject_MakeTpCall in /usr/bin/python3 +184: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 46# 0x00000000005335D0 in /usr/bin/python3 +184: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 48# 0x00000000004AC3B4 in /usr/bin/python3 +184: 49# 0x0000000000665934 in /usr/bin/python3 +184: 50# _PyObject_MakeTpCall in /usr/bin/python3 +184: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 52# 0x0000000000505090 in /usr/bin/python3 +184: 53# _PyObject_MakeTpCall in /usr/bin/python3 +184: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 +184: 55# PyEval_EvalCode in /usr/bin/python3 +184: 56# 0x00000000005FFD24 in /usr/bin/python3 +184: 57# 0x00000000005F9904 in /usr/bin/python3 +184: 58# 0x0000000000627ED4 in /usr/bin/python3 +184: 59# 0x0000000000627274 in /usr/bin/python3 +184: 60# 0x0000000000627010 in /usr/bin/python3 +184: 61# Py_RunMain in /usr/bin/python3 +184: 62# Py_BytesMain in /usr/bin/python3 +184: 63# 0x0000FFFF935D229C in /lib/aarch64-linux-gnu/libc.so.6 +184: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 +184: 65# _start in /usr/bin/python3 +184: ---------- +184: **** +184: +191/235 Test #202: molStandardizeTest ..................... Passed 4.11 sec test 203 Start 203: molNormalizeTest 203: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 203: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 203: Test timeout computed to be: 1500 -203: [05:51:57] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -203: [05:51:57] Initializing Normalizer -203: [05:51:57] Running Normalizer -203: [05:51:57] Rule applied: BrokenazidetoN=N+=N- -203: [05:51:57] Initializing Normalizer -203: [05:51:57] Running Normalizer -203: [05:51:57] Initializing Normalizer -203: [05:51:57] Running Normalizer -192/235 Test #203: molNormalizeTest ....................... Passed 0.19 sec +203: [15:24:19] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +203: [15:24:19] Initializing Normalizer +203: [15:24:19] Running Normalizer +203: [15:24:19] Rule applied: BrokenazidetoN=N+=N- +203: [15:24:19] Initializing Normalizer +203: [15:24:19] Running Normalizer +203: [15:24:19] Initializing Normalizer +203: [15:24:19] Running Normalizer +192/235 Test #203: molNormalizeTest ....................... Passed 0.10 sec test 204 Start 204: molValidateTest @@ -33821,71 +34008,157 @@ 204: ERROR: [StereoValidation] Bond 3 has assigned stereo type, but unexpected bond order. 204: there 204: ERROR: [StereoValidation] Atom 0 has stereo bonds, but less than 3 explicit substituents. -193/235 Test #204: molValidateTest ........................ Passed 0.07 sec +193/235 Test #204: molValidateTest ........................ Passed 0.04 sec test 205 Start 205: molChargeTest 205: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 205: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 205: Test timeout computed to be: 1500 -194/235 Test #205: molChargeTest .......................... Passed 0.23 sec +194/235 Test #205: molChargeTest .......................... Passed 0.06 sec test 206 Start 206: molTautomerTest 206: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 206: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 206: Test timeout computed to be: 1500 -206: [05:51:58] Tautomer enumeration stopped at 292 tautomers: max transforms reached -173: Query 2 -206: [05:51:59] Tautomer enumeration stopped at 292 tautomers: max transforms reached -206: [05:51:59] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -206: [05:51:59] Tautomer enumeration stopped at 50 tautomers: canceled +206: [15:24:20] Tautomer enumeration stopped at 292 tautomers: max transforms reached +206: [15:24:20] Tautomer enumeration stopped at 292 tautomers: max transforms reached +206: [15:24:20] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +206: [15:24:20] Tautomer enumeration stopped at 33 tautomers: canceled 206: Enumeration was canceled due to timeout (50 ms) -206: 375 -206: Enumeration has completed -206: [05:52:00] Tautomer enumeration stopped at 53 tautomers: canceled -206: CN=c1cc[nH]cn1 -206: CN=c1ccnc[nH]1 -206: CNc1ccncn1 -206: res: CNc1ccncn1 -206: CN=c1cccc[nH]1 -206: CNc1ccccn1 -206: res: CNc1ccccn1 -195/235 Test #206: molTautomerTest ........................ Passed 4.00 sec +195/235 Test #198: pyTestThreads .......................... Passed 10.33 sec test 207 Start 207: molStandardizeSmallTest 207: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 207: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 207: Test timeout computed to be: 1500 -147: [05:52:02] UFFTYPER: Unrecognized atom type: S_6+6 (0) -147: [05:52:02] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -147: [05:52:02] UFFTYPER: Unrecognized charge state for atom: 0 -196/235 Test #207: molStandardizeSmallTest ................ Passed 0.08 sec +196/235 Test #207: molStandardizeSmallTest ................ Passed 0.12 sec test 208 Start 208: molFragmentTest 208: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 208: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 208: Test timeout computed to be: 1500 -208: [05:52:02] SMARTS Parse Error: syntax error while parsing: [Cl -208: [05:52:02] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -197/235 Test #208: molFragmentTest ........................ Passed 0.11 sec +208: [15:24:22] SMARTS Parse Error: syntax error while parsing: [Cl +208: [15:24:22] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +197/235 Test #208: molFragmentTest ........................ Passed 0.09 sec test 209 Start 209: molStandardizeCatchTest 209: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 209: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 209: Test timeout computed to be: 1500 -209: Randomness seeded to: 1602363579 +209: Randomness seeded to: 2879556809 209: * - * - * - * m1 209: * - * - * - * m2 +206: 375 +206: Enumeration has completed 209: * - * - * - * m1 209: * - * - * - * m2 -209: [05:52:02] Can't kekulize mol. Unkekulized atoms: 3 7 -209: [05:52:02] Can't kekulize mol. Unkekulized atoms: 3 8 -209: [05:52:02] Can't kekulize mol. Unkekulized atoms: 2 3 4 -194: ..[05:52:02] +209: [15:24:23] Can't kekulize mol. Unkekulized atoms: 3 7 +209: [15:24:23] Can't kekulize mol. Unkekulized atoms: 3 8 +209: [15:24:23] Can't kekulize mol. Unkekulized atoms: 2 3 4 +206: [15:24:23] Tautomer enumeration stopped at 63 tautomers: canceled +206: CN=c1cc[nH]cn1 +206: CN=c1ccnc[nH]1 +206: CNc1ccncn1 +206: res: CNc1ccncn1 +206: CN=c1cccc[nH]1 +206: CNc1ccccn1 +206: res: CNc1ccccn1 +198/235 Test #206: molTautomerTest ........................ Passed 6.19 sec +test 210 + Start 210: molStandardizePipelineTest + +210: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest +210: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize +210: Test timeout computed to be: 1500 +210: Randomness seeded to: 2563615675 +210: 1 Counts line too short: '' on line4 +210: 1 Could not instantiate a valid molecule from input +210: 8 Molecule has no atoms +210: [15:24:26] Explicit valence for atom # 1 N, 4, is greater than permitted +210: [15:24:26] Explicit valence for atom # 1 N, 4, is greater than permitted +210: 8 Explicit valence for atom # 1 N, 4, is greater than permitted +210: 128 An error occurred while preparing the molecule for standardization. +210: 8 The molecule contains an unknown isotope: 3C +210: 4 Query atom 0 is not allowed +210: 4 Bond 0 of aromatic type is not allowed +210: 4 Bond 1 of aromatic type is not allowed +210: 4 Bond 2 of aromatic type is not allowed +210: 4 Bond 3 of aromatic type is not allowed +210: 4 Bond 5 of aromatic type is not allowed +210: 4 Bond 6 of aromatic type is not allowed +210: 4 Bond 2 of dative type is not allowed +210: 4 Bond 3 of dative type is not allowed +210: 4 Enhanced stereochemistry features are not allowed +210: 8 The radical at atom 0 is not allowed +210: [15:24:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +210: 16 The molecule includes non-null Z coordinates +210: 32 Atom 0 too close to bond 2 +210: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit +210: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds +210: 64 Atom 0 has adjacent stereo bonds with like orientation +210: [15:24:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +210: 16 The molecule includes non-null Z coordinates +210: 64 Atom 0 has adjacent stereo bonds with like orientation +210: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit +210: 8388608 One or more metal atoms were disconnected. +210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +210: 67108864 The protonation state was adjusted. +210: 16777216 The representation of some functional groups was adjusted. +210: 67108864 The protonation state was adjusted. +210: 16777216 The representation of some functional groups was adjusted. +210: 67108864 The protonation state was adjusted. +210: 16777216 The representation of some functional groups was adjusted. +210: 16777216 The representation of some functional groups was adjusted. +210: 67108864 The protonation state was adjusted. +210: 16777216 The representation of some functional groups was adjusted. +210: 67108864 The protonation state was adjusted. +210: 16777216 The representation of some functional groups was adjusted. +210: 67108864 The protonation state was adjusted. +210: 16777216 The representation of some functional groups was adjusted. +210: 67108864 The protonation state was adjusted. +210: 8388608 One or more metal atoms were disconnected. +210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +210: 67108864 The protonation state was adjusted. +210: 8388608 One or more metal atoms were disconnected. +210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +210: 67108864 The protonation state was adjusted. +210: 8388608 One or more metal atoms were disconnected. +210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +210: 67108864 The protonation state was adjusted. +210: 8388608 One or more metal atoms were disconnected. +210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +210: 67108864 The protonation state was adjusted. +210: 8388608 One or more metal atoms were disconnected. +210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. +210: 67108864 The protonation state was adjusted. +210: 16777216 The "wavy" style of bond 4 was removed +210: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration +210: 16777216 The "wavy" style of bond 2 was removed +210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +210: 16777216 The "wavy" style of bond 1 was removed +210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +210: 16777216 The "wavy" style of bond 1 was removed +210: 16777216 The "wavy" style of bond 4 was removed +210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration +210: 16777216 The "wavy" style of bond 3 was removed +210: 16777216 The representation of some functional groups was adjusted. +210: [15:24:26] Can't kekulize mol. Unkekulized atoms: 2 3 5 +210: =============================================================================== +210: All tests passed (268 assertions in 5 test cases) +210: +199/235 Test #210: molStandardizePipelineTest ............. Passed 0.72 sec +test 211 + Start 211: pyMolStandardize + +211: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +211: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +211: Test timeout computed to be: 1500 +194: ..[15:24:27] 194: 194: **** 194: Pre-condition Violation @@ -33899,7 +34172,7 @@ 194: 2# RDKit::Atom::getOwningMol() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl, boost::mpl::vector2 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33910,17 +34183,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -33952,13 +34225,13 @@ 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [05:52:02] +194: [15:24:27] 194: 194: **** 194: Pre-condition Violation @@ -33972,7 +34245,7 @@ 194: 2# RDKit::AtomGetNeighbors(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -33983,17 +34256,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -34025,13 +34298,13 @@ 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [05:52:02] +194: [15:24:27] 194: 194: **** 194: Pre-condition Violation @@ -34045,7 +34318,7 @@ 194: 2# RDKit::AtomGetBonds(RDKit::Atom*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34056,17 +34329,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -34098,13 +34371,13 @@ 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [05:52:02] +194: [15:24:27] 194: 194: **** 194: Pre-condition Violation @@ -34118,7 +34391,7 @@ 194: 2# RDKit::AtomIsInRing(RDKit::Atom const*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34129,17 +34402,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -34171,13 +34444,13 @@ 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: [05:52:02] +194: [15:24:27] 194: 194: **** 194: Pre-condition Violation @@ -34191,7 +34464,7 @@ 194: 2# RDKit::AtomIsInRingSize(RDKit::Atom const*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34202,17 +34475,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -34244,13 +34517,13 @@ 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: .....[05:52:02] +194: .....[15:24:27] 194: 194: **** 194: Range Error @@ -34264,7 +34537,7 @@ 194: 2# RDKit::RWMol::addBond(unsigned int, unsigned int, RDKit::Bond::BondType) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34275,17 +34548,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -34317,49 +34590,49 @@ 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: ......[05:52:03] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -194: [05:52:03] ERROR: Smiles parse error on line 0 -194: [05:52:03] ERROR: Cannot create molecule from : 'c1ccccc' -194: [05:52:03] SMILES Parse Error: extra open parentheses while parsing: C(C -194: [05:52:03] SMILES Parse Error: check for mistakes around position 2: -194: [05:52:03] C(C -194: [05:52:03] ~^ -194: [05:52:03] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -194: [05:52:03] ERROR: Smiles parse error on line 3 -194: [05:52:03] ERROR: Cannot create molecule from : 'C(C' -194: [05:52:03] Explicit valence for atom # 1 C, 5, is greater than permitted -194: [05:52:03] ERROR: Could not sanitize molecule on line 6 -194: [05:52:03] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -194: [05:52:03] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -194: [05:52:03] ERROR: Smiles parse error on line 0 -194: [05:52:03] ERROR: Cannot create molecule from : 'c1ccccc' -194: [05:52:03] SMILES Parse Error: extra open parentheses while parsing: C(C -194: [05:52:03] SMILES Parse Error: check for mistakes around position 2: -194: [05:52:03] C(C -194: [05:52:03] ~^ -194: [05:52:03] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' -194: [05:52:03] ERROR: Smiles parse error on line 3 -194: [05:52:03] ERROR: Cannot create molecule from : 'C(C' -194: [05:52:03] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -194: [05:52:03] ERROR: Smiles parse error on line 6 -194: [05:52:03] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -194: [05:52:03] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] ERROR: Could not sanitize molecule ending on line 21 -194: [05:52:03] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] ERROR: EOF hit while reading atoms -194: [05:52:03] ERROR: moving to the beginning of the next molecule -194: [05:52:03] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] ERROR: Could not sanitize molecule ending on line 21 -194: [05:52:03] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] ERROR: EOF hit while reading atoms -194: [05:52:03] ERROR: moving to the beginning of the next molecule -194: ....[05:52:03] +194: ......[15:24:27] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +194: [15:24:27] ERROR: Smiles parse error on line 0 +194: [15:24:27] ERROR: Cannot create molecule from : 'c1ccccc' +194: [15:24:27] SMILES Parse Error: extra open parentheses while parsing: C(C +194: [15:24:27] SMILES Parse Error: check for mistakes around position 2: +194: [15:24:27] C(C +194: [15:24:27] ~^ +194: [15:24:27] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +194: [15:24:27] ERROR: Smiles parse error on line 3 +194: [15:24:27] ERROR: Cannot create molecule from : 'C(C' +194: [15:24:27] Explicit valence for atom # 1 C, 5, is greater than permitted +194: [15:24:27] ERROR: Could not sanitize molecule on line 6 +194: [15:24:27] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +194: [15:24:27] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +194: [15:24:27] ERROR: Smiles parse error on line 0 +194: [15:24:27] ERROR: Cannot create molecule from : 'c1ccccc' +194: [15:24:27] SMILES Parse Error: extra open parentheses while parsing: C(C +194: [15:24:27] SMILES Parse Error: check for mistakes around position 2: +194: [15:24:27] C(C +194: [15:24:27] ~^ +194: [15:24:27] SMILES Parse Error: Failed parsing SMILES 'C(C' for input: 'C(C' +194: [15:24:27] ERROR: Smiles parse error on line 3 +194: [15:24:27] ERROR: Cannot create molecule from : 'C(C' +194: [15:24:27] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +194: [15:24:27] ERROR: Smiles parse error on line 6 +194: [15:24:27] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +194: [15:24:27] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:27] ERROR: Could not sanitize molecule ending on line 21 +194: [15:24:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:27] ERROR: EOF hit while reading atoms +194: [15:24:27] ERROR: moving to the beginning of the next molecule +194: [15:24:27] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:27] ERROR: Could not sanitize molecule ending on line 21 +194: [15:24:27] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:27] ERROR: EOF hit while reading atoms +194: [15:24:27] ERROR: moving to the beginning of the next molecule +194: ....[15:24:27] 194: 194: **** 194: Pre-condition Violation @@ -34373,7 +34646,7 @@ 194: 2# RDKit::RingInfo::numRings() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34384,17 +34657,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -34426,13 +34699,13 @@ 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: .............[05:52:03] +194: .............[15:24:27] 194: 194: **** 194: Range Error @@ -34446,7 +34719,7 @@ 194: 2# RDKit::ROMol::getAtomWithIdx(unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 194: 3# boost::python::objects::caller_py_function_impl >, boost::mpl::vector3 > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 4# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 5# 0x0000FFFFB2662680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 5# 0x0000FFFFB8DA2680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 6# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 7# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdSLNParse.so 194: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdChemReactions.so @@ -34457,17 +34730,17 @@ 194: 13# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so 194: 14# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so 194: 15# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 16# 0x0000FFFFB0B9B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 17# 0x0000FFFFB0B9B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 18# 0x0000FFFFB0B9B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 19# 0x0000FFFFB0B9B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -194: 20# 0x0000FFFFB0B9B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 16# 0x0000FFFFB72DB360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 17# 0x0000FFFFB72DB2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 18# 0x0000FFFFB72DB288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 19# 0x0000FFFFB72DB220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so +194: 20# 0x0000FFFFB72DB1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so 194: 21# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 22# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 23# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 24# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 194: 25# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -194: 26# 0x0000FFFFB265F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +194: 26# 0x0000FFFFB8D9F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 194: 27# _PyObject_MakeTpCall in /usr/bin/python3 194: 28# _PyEval_EvalFrameDefault in /usr/bin/python3 194: 29# 0x00000000005335D0 in /usr/bin/python3 @@ -34499,483 +34772,241 @@ 194: 55# 0x0000000000627010 in /usr/bin/python3 194: 56# Py_RunMain in /usr/bin/python3 194: 57# Py_BytesMain in /usr/bin/python3 -194: 58# 0x0000FFFFB33A229C in /lib/aarch64-linux-gnu/libc.so.6 +194: 58# 0x0000FFFFB9AE229C in /lib/aarch64-linux-gnu/libc.so.6 194: 59# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 194: 60# _start in /usr/bin/python3 194: ---------- 194: **** 194: -194: ...[05:52:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -194: ............................[05:52:03] SMILES Parse Error: unclosed ring for input: 'C1CC' -194: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| -194: 551 -194: ..[05:52:03] WARNING: not removing hydrogen atom without neighbors -194: [05:52:03] WARNING: not removing hydrogen atom with dummy atom neighbors -194: [05:52:03] WARNING: not removing hydrogen atom with wedged bond -194: [05:52:03] WARNING: not removing hydrogen atom without neighbors -194: [05:52:03] WARNING: not removing hydrogen atom with dummy atom neighbors -194: ......[05:52:03] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 -194: .[05:52:03] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] Explicit valence for atom # 1 F, 2, is greater than permitted -194: [05:52:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 -194: [05:52:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 -194: [05:52:03] Can't kekulize mol. Unkekulized atoms: 0 1 2 +194: ...[15:24:27] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 150: --------------------------------- 150: test getO3AForProbeConfs 150: 150: *********************************************************** -198/235 Test #150: testO3AAlign ........................... Passed 42.61 sec -test 210 - Start 210: molStandardizePipelineTest +200/235 Test #150: testO3AAlign ........................... Passed 66.38 sec +test 212 + Start 212: testScaffoldNetwork -210: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizePipelineTest -210: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize -210: Test timeout computed to be: 1500 -194: ..........[05:52:03] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -194: [05:52:03] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -194: .[05:52:03] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -194: [05:52:03] SMILES Parse Error: check for mistakes around position 4: -194: [05:52:03] CCC |$foo;;bar$| ourname -194: [05:52:03] ~~~^ -194: [05:52:03] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -194: ..[05:52:03] SMILES Parse Error: syntax error while parsing: error -194: [05:52:03] SMILES Parse Error: check for mistakes around position 1: -194: [05:52:03] error -194: [05:52:03] ^ -194: [05:52:03] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -194: [05:52:03] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -194: [05:52:03] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -194: [05:52:03] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -210: Randomness seeded to: 3880104527 -210: 1 Counts line too short: '' on line4 -210: 1 Could not instantiate a valid molecule from input -210: 8 Molecule has no atoms -210: [05:52:03] Explicit valence for atom # 1 N, 4, is greater than permitted -210: [05:52:03] Explicit valence for atom # 1 N, 4, is greater than permitted -210: 8 Explicit valence for atom # 1 N, 4, is greater than permitted -210: 128 An error occurred while preparing the molecule for standardization. -210: 8 The molecule contains an unknown isotope: 3C -210: 4 Query atom 0 is not allowed -210: 4 Bond 0 of aromatic type is not allowed -210: 4 Bond 1 of aromatic type is not allowed -210: 4 Bond 2 of aromatic type is not allowed -210: 4 Bond 3 of aromatic type is not allowed -210: 4 Bond 5 of aromatic type is not allowed -210: 4 Bond 6 of aromatic type is not allowed -210: 4 Bond 2 of dative type is not allowed -210: 4 Bond 3 of dative type is not allowed -210: 4 Enhanced stereochemistry features are not allowed -210: 8 The radical at atom 0 is not allowed -210: [05:52:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -210: 16 The molecule includes non-null Z coordinates -210: 32 Atom 0 too close to bond 2 -210: 32 The length of bond 3 between atoms 0 and 3 exceeds a configured limit -194: .........................[05:52:03] SMILES Parse Error: syntax error while parsing: garbage_0 -194: [05:52:03] SMILES Parse Error: check for mistakes around position 1: -194: [05:52:03] garbage_0 -194: [05:52:03] ^ -194: [05:52:03] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -194: [05:52:03] SMILES Parse Error: syntax error while parsing: garbage_2 -194: [05:52:03] SMILES Parse Error: check for mistakes around position 1: -194: [05:52:03] garbage_2 -194: [05:52:03] ^ -194: [05:52:03] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -194: [05:52:03] SMILES Parse Error: syntax error while parsing: garbage_4 -194: [05:52:03] SMILES Parse Error: check for mistakes around position 1: -194: [05:52:03] garbage_4 -194: [05:52:03] ^ -194: [05:52:03] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -210: 64 Atom 0 has 3 explicit substituents and multiple stereo bonds -210: 64 Atom 0 has adjacent stereo bonds with like orientation -210: [05:52:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -210: 16 The molecule includes non-null Z coordinates -210: 64 Atom 0 has adjacent stereo bonds with like orientation -210: 32 The length of bond 16 between atoms 16 and 1 exceeds a configured limit -210: 8388608 One or more metal atoms were disconnected. -210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -210: 67108864 The protonation state was adjusted. +212: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +212: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork +212: Test timeout computed to be: 1500 +194: ............................[15:24:28] SMILES Parse Error: unclosed ring for input: 'C1CC' +194: ......smi: CC1=C(n2cccc2[C@H](C)Cl)C(C)CCC1 |(2.679,0.4142,;1.3509,1.181,;0.0229,0.4141,;0.0229,-1.1195,;1.2645,-2.0302,;0.7901,-3.4813,;-0.7446,-3.4813,;-1.219,-2.0302,;-2.679,-1.5609,;-3.0039,-0.0556,;-3.8202,-2.595,;-1.3054,1.1809,;-2.6335,0.4141,;-1.3054,2.7145,;0.0229,3.4813,;1.3509,2.7146,),wD:8.9,2.11,a:2,&1:8| +194: 561 +194: ..[15:24:28] WARNING: not removing hydrogen atom without neighbors +194: [15:24:28] WARNING: not removing hydrogen atom with dummy atom neighbors +194: [15:24:28] WARNING: not removing hydrogen atom with wedged bond +194: [15:24:28] WARNING: not removing hydrogen atom without neighbors +194: [15:24:28] WARNING: not removing hydrogen atom with dummy atom neighbors +194: ......[15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 +194: .[15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:28] Explicit valence for atom # 1 F, 2, is greater than permitted +194: [15:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 +194: [15:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 +194: [15:24:28] Can't kekulize mol. Unkekulized atoms: 0 1 2 +211: .....[15:24:28] Tautomer enumeration stopped at 292 tautomers: max transforms reached +194: ..........[15:24:29] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +194: [15:24:29] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +194: .[15:24:29] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +194: [15:24:29] SMILES Parse Error: check for mistakes around position 4: +194: [15:24:29] CCC |$foo;;bar$| ourname +194: [15:24:29] ~~~^ +194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +194: ..[15:24:29] SMILES Parse Error: syntax error while parsing: error +194: [15:24:29] SMILES Parse Error: check for mistakes around position 1: +194: [15:24:29] error +194: [15:24:29] ^ +194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +194: [15:24:29] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +194: [15:24:29] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +211: [15:24:29] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +194: .........................[15:24:29] SMILES Parse Error: syntax error while parsing: garbage_0 +194: [15:24:29] SMILES Parse Error: check for mistakes around position 1: +194: [15:24:29] garbage_0 +194: [15:24:29] ^ +194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +194: [15:24:29] SMILES Parse Error: syntax error while parsing: garbage_2 +194: [15:24:29] SMILES Parse Error: check for mistakes around position 1: +194: [15:24:29] garbage_2 +194: [15:24:29] ^ +194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +194: [15:24:29] SMILES Parse Error: syntax error while parsing: garbage_4 +194: [15:24:29] SMILES Parse Error: check for mistakes around position 1: +194: [15:24:29] garbage_4 +194: [15:24:29] ^ +194: [15:24:29] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' 194: ............ 194: ---------------------------------------------------------------------- -194: Ran 279 tests in 9.940s +194: Ran 279 tests in 18.187s 194: 194: OK 194: supplier: 194: supplier: 194: supplier: -210: 16777216 The representation of some functional groups was adjusted. -210: 67108864 The protonation state was adjusted. -210: 16777216 The representation of some functional groups was adjusted. -210: 67108864 The protonation state was adjusted. -210: 16777216 The representation of some functional groups was adjusted. -210: 16777216 The representation of some functional groups was adjusted. -210: 67108864 The protonation state was adjusted. -210: 16777216 The representation of some functional groups was adjusted. -210: 67108864 The protonation state was adjusted. -210: 16777216 The representation of some functional groups was adjusted. -210: 67108864 The protonation state was adjusted. -210: 16777216 The representation of some functional groups was adjusted. -210: 67108864 The protonation state was adjusted. -210: 8388608 One or more metal atoms were disconnected. -210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -210: 67108864 The protonation state was adjusted. -210: 8388608 One or more metal atoms were disconnected. -210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -210: 67108864 The protonation state was adjusted. -210: 8388608 One or more metal atoms were disconnected. -210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -210: 67108864 The protonation state was adjusted. -210: 8388608 One or more metal atoms were disconnected. -210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -210: 67108864 The protonation state was adjusted. -210: 8388608 One or more metal atoms were disconnected. -210: 33554432 One or more disconnected fragments (e.g., counterions) were removed. -210: 67108864 The protonation state was adjusted. -210: 16777216 The "wavy" style of bond 4 was removed -210: 16777216 Double bond 1 was assigned an undefined/unknown stereochemical configuration -210: 16777216 The "wavy" style of bond 2 was removed -210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -210: 16777216 The "wavy" style of bond 1 was removed -210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -210: 16777216 The "wavy" style of bond 1 was removed -210: 16777216 The "wavy" style of bond 4 was removed -210: 16777216 Double bond 2 was assigned an undefined/unknown stereochemical configuration -210: 16777216 The "wavy" style of bond 3 was removed -210: 16777216 The representation of some functional groups was adjusted. -210: [05:52:03] Can't kekulize mol. Unkekulized atoms: 2 3 5 -210: =============================================================================== -210: All tests passed (268 assertions in 5 test cases) -210: -199/235 Test #210: molStandardizePipelineTest ............. Passed 0.26 sec -test 211 - Start 211: pyMolStandardize - -211: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -211: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -211: Test timeout computed to be: 1500 -200/235 Test #194: pyGraphMolWrap ......................... Passed 10.67 sec -test 212 - Start 212: testScaffoldNetwork - -212: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -212: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork -212: Test timeout computed to be: 1500 -184: ......[05:52:04] -184: -184: **** -184: Pre-condition Violation -184: RingInfo not initialized -184: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -184: Failed Expression: df_init -184: ---------- -184: Stacktrace: -184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -184: 2# RDKit::RingInfo::numAtomRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -184: 3# RDKit::AtomRingQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSmilesParse.so.1 -184: 4# Queries::AndQuery::Match(RDKit::Atom const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -184: 5# RDKit::atomCompat(RDKit::Atom const*, RDKit::Atom const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 8# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 9# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 10# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 11# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 12# 0x0000FFFFAB0DEB90 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 13# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 14# 0x0000FFFFACB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 15# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 16# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -184: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -184: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -184: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 20# 0x0000FFFFAB03B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 21# 0x0000FFFFAB03B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 22# 0x0000FFFFAB03B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 23# 0x0000FFFFAB03B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 24# 0x0000FFFFAB03B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 25# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -184: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -184: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -184: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -184: 29# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 30# 0x0000FFFFACB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 31# _PyObject_MakeTpCall in /usr/bin/python3 -184: 32# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 33# 0x00000000005335D0 in /usr/bin/python3 -184: 34# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 35# 0x00000000004AC3B4 in /usr/bin/python3 -184: 36# 0x0000000000665934 in /usr/bin/python3 -184: 37# _PyObject_MakeTpCall in /usr/bin/python3 -184: 38# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 39# 0x00000000005335D0 in /usr/bin/python3 -184: 40# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 41# 0x00000000004AC3B4 in /usr/bin/python3 -184: 42# 0x0000000000665934 in /usr/bin/python3 -184: 43# _PyObject_MakeTpCall in /usr/bin/python3 -184: 44# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 45# 0x00000000005335D0 in /usr/bin/python3 -184: 46# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 47# 0x00000000004AC3B4 in /usr/bin/python3 -184: 48# 0x0000000000665934 in /usr/bin/python3 -184: 49# _PyObject_MakeTpCall in /usr/bin/python3 -184: 50# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 51# 0x0000000000505090 in /usr/bin/python3 -184: 52# _PyObject_MakeTpCall in /usr/bin/python3 -184: 53# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 54# PyEval_EvalCode in /usr/bin/python3 -184: 55# 0x00000000005FFD24 in /usr/bin/python3 -184: 56# 0x00000000005F9904 in /usr/bin/python3 -184: 57# 0x0000000000627ED4 in /usr/bin/python3 -184: 58# 0x0000000000627274 in /usr/bin/python3 -184: 59# 0x0000000000627010 in /usr/bin/python3 -184: 60# Py_RunMain in /usr/bin/python3 -184: 61# Py_BytesMain in /usr/bin/python3 -184: 62# 0x0000FFFFAD52229C in /lib/aarch64-linux-gnu/libc.so.6 -184: 63# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -184: 64# _start in /usr/bin/python3 -184: ---------- -184: **** -184: -184: [05:52:04] -184: -184: **** -184: Pre-condition Violation -184: RingInfo not initialized -184: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -184: Failed Expression: df_init -184: ---------- -184: Stacktrace: -184: 0# Invar::Invariant::toString[abi:cxx11]() const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -184: 1# Invar::operator<<(std::ostream&, Invar::Invariant const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitRDGeneral.so.1 -184: 2# RDKit::RingInfo::numBondRings(unsigned int) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -184: 3# 0x0000FFFFAAB92FA8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -184: 4# Queries::EqualityQuery::Match(RDKit::Bond const*) const in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitGraphMol.so.1 -184: 5# RDKit::bondCompat(RDKit::Bond const*, RDKit::Bond const*, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 6# boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::IsFeasiblePair(unsigned int, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 7# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 8# bool boost::detail::VF2SubState const, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor>::MatchAll, std::allocator > >, std::allocator, std::allocator > > > > >(unsigned int*, unsigned int*, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 9# bool boost::vf2_all, RDKit::detail::AtomLabelFunctor, RDKit::detail::BondLabelFunctor, RDKit::MolMatchFinalCheckFunctor, std::vector, std::allocator > >, std::allocator, std::allocator > > > > >(boost::adjacency_list const&, boost::adjacency_list const&, RDKit::detail::AtomLabelFunctor&, RDKit::detail::BondLabelFunctor&, RDKit::MolMatchFinalCheckFunctor&, std::vector, std::allocator > >, std::allocator, std::allocator > > > >&, unsigned int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 10# RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, RDKit::SubstructMatchParameters const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu//lib/libRDKitSubstructMatch.so.1 -184: 11# bool RDKit::SubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, std::vector, std::allocator > >&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 12# bool RDKit::HasSubstructMatch(RDKit::ROMol const&, RDKit::ROMol const&, bool, bool, bool) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 13# 0x0000FFFFAB0DEB90 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 14# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 15# 0x0000FFFFACB42680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 16# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 17# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -184: 18# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdmolfiles.so -184: 19# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdCIPLabeler.so -184: 20# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 21# 0x0000FFFFAB03B360 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 22# 0x0000FFFFAB03B2F8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 23# 0x0000FFFFAB03B288 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 24# 0x0000FFFFAB03B220 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 25# 0x0000FFFFAB03B1B8 in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/Chem/rdchem.so -184: 26# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -184: 27# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -184: 28# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -184: 29# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so -184: 30# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 31# 0x0000FFFFACB3F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -184: 32# _PyObject_MakeTpCall in /usr/bin/python3 -184: 33# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 34# 0x00000000005335D0 in /usr/bin/python3 -184: 35# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 36# 0x00000000004AC3B4 in /usr/bin/python3 -184: 37# 0x0000000000665934 in /usr/bin/python3 -184: 38# _PyObject_MakeTpCall in /usr/bin/python3 -184: 39# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 40# 0x00000000005335D0 in /usr/bin/python3 -184: 41# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 42# 0x00000000004AC3B4 in /usr/bin/python3 -184: 43# 0x0000000000665934 in /usr/bin/python3 -184: 44# _PyObject_MakeTpCall in /usr/bin/python3 -184: 45# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 46# 0x00000000005335D0 in /usr/bin/python3 -184: 47# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 48# 0x00000000004AC3B4 in /usr/bin/python3 -184: 49# 0x0000000000665934 in /usr/bin/python3 -184: 50# _PyObject_MakeTpCall in /usr/bin/python3 -184: 51# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 52# 0x0000000000505090 in /usr/bin/python3 -184: 53# _PyObject_MakeTpCall in /usr/bin/python3 -184: 54# _PyEval_EvalFrameDefault in /usr/bin/python3 -184: 55# PyEval_EvalCode in /usr/bin/python3 -184: 56# 0x00000000005FFD24 in /usr/bin/python3 -184: 57# 0x00000000005F9904 in /usr/bin/python3 -184: 58# 0x0000000000627ED4 in /usr/bin/python3 -184: 59# 0x0000000000627274 in /usr/bin/python3 -184: 60# 0x0000000000627010 in /usr/bin/python3 -184: 61# Py_RunMain in /usr/bin/python3 -184: 62# Py_BytesMain in /usr/bin/python3 -184: 63# 0x0000FFFFAD52229C in /lib/aarch64-linux-gnu/libc.so.6 -184: 64# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 -184: 65# _start in /usr/bin/python3 -184: ---------- -184: **** -184: -211: .....[05:52:04] Tautomer enumeration stopped at 292 tautomers: max transforms reached -211: [05:52:04] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -211: .[05:52:05] Tautomer enumeration stopped at 71 tautomers: canceled -211: Enumeration was canceled due to timeout (50 ms) -212: Randomness seeded to: 979807935 -212: =============================================================================== -212: All tests passed (273 assertions in 19 test cases) -212: -201/235 Test #212: testScaffoldNetwork .................... Passed 2.09 sec +201/235 Test #194: pyGraphMolWrap ......................... Passed 19.40 sec test 213 Start 213: pyScaffoldNetwork 213: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 213: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 213: Test timeout computed to be: 1500 +211: .[15:24:30] Tautomer enumeration stopped at 21 tautomers: canceled +211: Enumeration was canceled due to timeout (50 ms) 213: ....... 213: ---------------------------------------------------------------------- -213: Ran 7 tests in 0.051s +213: Ran 7 tests in 0.169s 213: 213: OK -202/235 Test #213: pyScaffoldNetwork ...................... Passed 0.47 sec +202/235 Test #213: pyScaffoldNetwork ...................... Passed 1.48 sec test 214 Start 214: pyScaffoldNetworkPickling 214: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 214: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 214: Test timeout computed to be: 1500 -214: . -214: ---------------------------------------------------------------------- -214: Ran 1 test in 0.016s -214: -214: OK -203/235 Test #214: pyScaffoldNetworkPickling .............. Passed 0.45 sec +212: Randomness seeded to: 1858183942 +212: =============================================================================== +212: All tests passed (273 assertions in 19 test cases) +212: +203/235 Test #212: testScaffoldNetwork .................... Passed 3.67 sec test 215 Start 215: testMolEnumerator 215: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 215: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 215: Test timeout computed to be: 1500 -215: Randomness seeded to: 921738652 -215: [05:52:06] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +215: Randomness seeded to: 3481345342 +215: [15:24:31] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +211: Enumeration has completed +147: [15:24:31] UFFTYPER: Unrecognized atom type: S_6+6 (0) +147: [15:24:31] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +147: [15:24:31] UFFTYPER: Unrecognized charge state for atom: 0 +211: [15:24:31] Tautomer enumeration stopped at 31 tautomers: canceled 215: =============================================================================== 215: All tests passed (321 assertions in 16 test cases) 215: -204/235 Test #215: testMolEnumerator ...................... Passed 0.11 sec +204/235 Test #215: testMolEnumerator ...................... Passed 0.36 sec test 216 Start 216: pyMolEnumerator 216: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 216: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 216: Test timeout computed to be: 1500 -211: Enumeration has completed -211: [05:52:07] Tautomer enumeration stopped at 47 tautomers: canceled -216: ... -216: ---------------------------------------------------------------------- -216: Ran 3 tests in 0.016s -216: -216: OK -205/235 Test #216: pyMolEnumerator ........................ Passed 0.43 sec +214: . +214: ---------------------------------------------------------------------- +214: Ran 1 test in 0.036s +214: +214: OK +205/235 Test #214: pyScaffoldNetworkPickling .............. Passed 1.19 sec test 217 Start 217: testAbbreviations 217: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 217: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 217: Test timeout computed to be: 1500 -217: Randomness seeded to: 1598995702 -217: [05:52:07] SMARTS Parse Error: syntax error while parsing: *fail -217: [05:52:07] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -217: [05:52:07] no suitable SubstanceGroups found +211: ..........[15:24:32] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [15:24:32] Explicit valence for atom # 1 N, 4, is greater than permitted +211: [15:24:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +217: Randomness seeded to: 1593005015 +217: [15:24:32] SMARTS Parse Error: syntax error while parsing: *fail +217: [15:24:32] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +217: [15:24:32] no suitable SubstanceGroups found 217: =============================================================================== 217: All tests passed (195 assertions in 12 test cases) 217: -206/235 Test #217: testAbbreviations ...................... Passed 0.04 sec +206/235 Test #217: testAbbreviations ...................... Passed 0.17 sec test 218 Start 218: pyAbbreviations 218: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 218: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 218: Test timeout computed to be: 1500 -211: ..........[05:52:07] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [05:52:07] Explicit valence for atom # 1 N, 4, is greater than permitted -211: [05:52:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -211: [05:52:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -218: ....... -218: ---------------------------------------------------------------------- -218: Ran 7 tests in 0.015s -218: -218: OK -207/235 Test #218: pyAbbreviations ........................ Passed 0.25 sec +211: [15:24:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +216: ... +216: ---------------------------------------------------------------------- +216: Ran 3 tests in 0.056s +216: +216: OK +207/235 Test #216: pyMolEnumerator ........................ Passed 1.23 sec test 219 Start 219: generalizedSubstructCatch 219: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 219: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 219: Test timeout computed to be: 1500 -219: Randomness seeded to: 3758572600 -219: =============================================================================== -219: All tests passed (486 assertions in 10 test cases) -219: -208/235 Test #219: generalizedSubstructCatch .............. Passed 0.45 sec +218: ....... +218: ---------------------------------------------------------------------- +218: Ran 7 tests in 0.071s +218: +218: OK +208/235 Test #218: pyAbbreviations ........................ Passed 1.27 sec test 220 Start 220: pyGeneralizedSubstruct 220: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 220: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 220: Test timeout computed to be: 1500 -220: ....... -220: ---------------------------------------------------------------------- -220: Ran 7 tests in 0.260s -220: -220: OK -209/235 Test #220: pyGeneralizedSubstruct ................. Passed 0.87 sec +219: Randomness seeded to: 2719601452 +219: =============================================================================== +219: All tests passed (486 assertions in 10 test cases) +219: +209/235 Test #219: generalizedSubstructCatch .............. Passed 1.07 sec test 221 Start 221: testMolProcessing 221: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/testMolProcessing 221: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing 221: Test timeout computed to be: 1500 -211: ............[05:52:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -211: [05:52:09] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -211: [05:52:09] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. -211: ........[05:52:09] Explicit valence for atom # 1 O, 3, is greater than permitted -211: .. -211: ---------------------------------------------------------------------- -211: Ran 38 tests in 5.440s -211: -211: OK -211: done -210/235 Test #211: pyMolStandardize ....................... Passed 5.99 sec +220: ....... +220: ---------------------------------------------------------------------- +220: Ran 7 tests in 0.534s +220: +220: OK +210/235 Test #220: pyGeneralizedSubstruct ................. Passed 1.59 sec test 222 Start 222: pyMolProcessing 222: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolProcessing/Wrap/testMolProcessing.py" 222: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolProcessing/Wrap 222: Test timeout computed to be: 1500 -211/235 Test #198: pyTestThreads .......................... Passed 16.02 sec +211: ............[15:24:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +211: [15:24:35] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +211: [15:24:35] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 1 ignored. +211: ........[15:24:36] Explicit valence for atom # 1 O, 3, is greater than permitted +211: .. +211: ---------------------------------------------------------------------- +211: Ran 38 tests in 9.125s +211: +211: OK +211: done +222: .. +222: ---------------------------------------------------------------------- +222: Ran 2 tests in 0.735s +222: +222: OK +211/235 Test #211: pyMolStandardize ....................... Passed 10.53 sec test 223 Start 223: testMIF 223: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/testMIF 223: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields 223: Test timeout computed to be: 1500 -223: Randomness seeded to: 23957717 -223: =============================================================================== -223: All tests passed (27926 assertions in 8 test cases) -223: -212/235 Test #223: testMIF ................................ Passed 0.16 sec +212/235 Test #222: pyMolProcessing ........................ Passed 1.97 sec test 224 Start 224: pyMIF 224: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/GraphMol/MolInteractionFields/Wrap/testMIF.py" 224: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/GraphMol/MolInteractionFields/Wrap 224: Test timeout computed to be: 1500 -222: .. -222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.619s -222: -222: OK -213/235 Test #222: pyMolProcessing ........................ Passed 1.29 sec +223: Randomness seeded to: 3058970526 +223: =============================================================================== +223: All tests passed (27926 assertions in 8 test cases) +223: +213/235 Test #223: testMIF ................................ Passed 0.28 sec test 225 Start 225: testQuery @@ -35015,7 +35046,7 @@ 226: ------------------------------------- 226: ExplicitFeatures 2D, string type. 226: done -215/235 Test #226: testBaseFeatures ....................... Passed 0.04 sec +215/235 Test #226: testBaseFeatures ....................... Passed 0.03 sec test 227 Start 227: testMatCalc @@ -35076,56 +35107,97 @@ 228: Test timeout computed to be: 1500 224: ....... 224: ---------------------------------------------------------------------- -224: Ran 7 tests in 0.129s +224: Ran 7 tests in 0.194s 224: 224: OK 224: Testing MIF wrapper -217/235 Test #224: pyMIF .................................. Passed 1.20 sec +217/235 Test #224: pyMIF .................................. Passed 1.36 sec test 229 Start 229: testSimDivPickers 229: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 229: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers 229: Test timeout computed to be: 1500 -229: [05:52:11] ------------------------------------- -229: [05:52:11] Testing github issue 1421: MaxMinPicker picking non-existent element. -229: [05:52:11] Done -229: [05:52:11] ------------------------------------- -229: [05:52:11] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -229: [05:52:11] Done -218/235 Test #229: testSimDivPickers ...................... Passed 0.06 sec +229: [15:24:38] ------------------------------------- +229: [15:24:38] Testing github issue 1421: MaxMinPicker picking non-existent element. +229: [15:24:38] Done +229: [15:24:38] ------------------------------------- +229: [15:24:38] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +229: [15:24:38] Done +218/235 Test #229: testSimDivPickers ...................... Passed 0.05 sec test 230 Start 230: pickersTestsCatch 230: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 230: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers 230: Test timeout computed to be: 1500 -230: Randomness seeded to: 4038834819 -230: =============================================================================== -230: All tests passed (21267 assertions in 1 test case) -230: -219/235 Test #230: pickersTestsCatch ...................... Passed 0.37 sec +184: ............. +184: ---------------------------------------------------------------------- +184: Ran 19 tests in 44.490s +184: +184: OK +184: Testing atom rings +184: testing bond rings +184: searching atom rings +184: searching bond rings +184: done +219/235 Test #184: pySubstructLibrary ..................... Passed 45.92 sec test 231 Start 231: pySimDivPickers 231: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/SimDivPickers/Wrap/testPickers.py" 231: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 231: Test timeout computed to be: 1500 -221: Randomness seeded to: 2970597158 -221: =============================================================================== -221: All tests passed (203 assertions in 1 test case) -221: -220/235 Test #221: testMolProcessing ...................... Passed 3.07 sec +230: Randomness seeded to: 187119721 +230: =============================================================================== +230: All tests passed (21267 assertions in 1 test case) +230: +220/235 Test #230: pickersTestsCatch ...................... Passed 0.73 sec test 232 Start 232: pyRanker 232: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ML/InfoTheory/Wrap/testRanker.py" 232: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 232: Test timeout computed to be: 1500 -231: [05:52:12] the useCache argument is deprecated and ignored -232: ..[05:52:12] +221: Randomness seeded to: 3426064245 +221: =============================================================================== +221: All tests passed (203 assertions in 1 test case) +221: +221/235 Test #221: testMolProcessing ...................... Passed 5.40 sec +test 233 + Start 233: testChemicalFeatures + +233: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures +233: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures +233: Test timeout computed to be: 1500 +233: ----------------------------------------- +233: Test1 +233: Done +222/235 Test #233: testChemicalFeatures ................... Passed 0.03 sec +test 234 + Start 234: pyFeatures + +234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/testFeatures.py" +234: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap +234: Test timeout computed to be: 1500 +231: [15:24:39] the useCache argument is deprecated and ignored +228: ..... +228: ---------------------------------------------------------------------- +228: Ran 5 tests in 1.754s +228: +228: OK +231: ...[15:24:40] the useCache argument is deprecated and ignored +231: [15:24:40] the useCache argument is deprecated and ignored +231: .[15:24:40] the useCache argument is deprecated and ignored +232: ..[15:24:40] 232: 232: **** +234: .. +234: ---------------------------------------------------------------------- +234: Ran 2 tests in 0.001s +234: +234: OK +234: Testing ChemicalFeatures Wrapper code: 232: Invariant Violation 232: Can't rank more bits than the ensemble size 232: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp @@ -35138,14 +35210,14 @@ 232: 3# RDInfoTheory::getTopNbits(RDInfoTheory::InfoBitRanker*, int) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 232: 4# boost::python::objects::caller_py_function_impl > >::operator()(_object*, _object*) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/ML/InfoTheory/rdInfoTheory.so 232: 5# boost::python::objects::function::call(_object*, _object*) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -232: 6# 0x0000FFFF9E132680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +232: 6# 0x0000FFFFAAE52680 in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 232: 7# boost::python::detail::exception_handler::operator()(boost::function0 const&) const in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 232: 8# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 232: 9# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 232: 10# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 232: 11# boost::detail::function::function_obj_invoker2, boost::_bi::list3, boost::arg<2>, boost::_bi::value > >, bool, boost::python::detail::exception_handler const&, boost::function0 const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0 const&) in /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/rdkit/rdBase.so 232: 12# boost::python::handle_exception_impl(boost::function0) in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 -232: 13# 0x0000FFFF9E12F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 +232: 13# 0x0000FFFFAAE4F25C in /lib/aarch64-linux-gnu/libboost_python313.so.1.83.0 232: 14# _PyObject_MakeTpCall in /usr/bin/python3 232: 15# _PyEval_EvalFrameDefault in /usr/bin/python3 232: 16# 0x00000000005335D0 in /usr/bin/python3 @@ -35177,7 +35249,7 @@ 232: 42# 0x0000000000627010 in /usr/bin/python3 232: 43# Py_RunMain in /usr/bin/python3 232: 44# Py_BytesMain in /usr/bin/python3 -232: 45# 0x0000FFFF9FA5229C in /lib/aarch64-linux-gnu/libc.so.6 +232: 45# 0x0000FFFFAC77229C in /lib/aarch64-linux-gnu/libc.so.6 232: 46# __libc_start_main in /lib/aarch64-linux-gnu/libc.so.6 232: 47# _start in /usr/bin/python3 232: ---------- @@ -35185,100 +35257,65 @@ 232: 232: ... 232: ---------------------------------------------------------------------- -232: Ran 5 tests in 0.032s +232: Ran 5 tests in 0.088s 232: 232: OK -228: ..... -228: ---------------------------------------------------------------------- -228: Ran 5 tests in 0.861s -228: -228: OK -221/235 Test #232: pyRanker ............................... Passed 0.39 sec -test 233 - Start 233: testChemicalFeatures - -233: Test command: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/testChemicalFeatures -233: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures -233: Test timeout computed to be: 1500 -222/235 Test #228: pyMatCalc .............................. Passed 1.25 sec -test 234 - Start 234: pyFeatures - -234: Test command: /usr/bin/python3 "/build/reproducible-path/rdkit-202409.6/Code/ChemicalFeatures/Wrap/testFeatures.py" -234: Working Directory: /build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap -234: Test timeout computed to be: 1500 -233: ----------------------------------------- -233: Test1 -233: Done -223/235 Test #233: testChemicalFeatures ................... Passed 0.05 sec +223/235 Test #228: pyMatCalc .............................. Passed 2.64 sec test 235 Start 235: pythonProjectTests 235: Test command: /usr/bin/python3 "-m" "pytest" 235: Working Directory: /build/reproducible-path/rdkit-202409.6/Projects 235: Test timeout computed to be: 1500 -231: ...[05:52:12] the useCache argument is deprecated and ignored -231: [05:52:12] the useCache argument is deprecated and ignored -231: .[05:52:12] the useCache argument is deprecated and ignored -234: .. -234: ---------------------------------------------------------------------- -234: Ran 2 tests in 0.010s -234: -234: OK -234: Testing ChemicalFeatures Wrapper code: -224/235 Test #234: pyFeatures ............................. Passed 0.68 sec +224/235 Test #232: pyRanker ............................... Passed 1.03 sec +225/235 Test #234: pyFeatures ............................. Passed 0.76 sec 231: ....... 231: ---------------------------------------------------------------------- -231: Ran 11 tests in 1.823s +231: Ran 11 tests in 3.026s 231: 231: OK -225/235 Test #231: pySimDivPickers ........................ Passed 2.36 sec +226/235 Test #231: pySimDivPickers ........................ Passed 3.89 sec 235: ============================= test session starts ============================== 235: platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0 235: rootdir: /build/reproducible-path/rdkit-202409.6/Projects 235: configfile: pytest.ini 235: collected 12 items 235: -146: [05:52:18] done -184: ............. -184: ---------------------------------------------------------------------- -184: Ran 19 tests in 35.521s -184: -184: OK -184: Testing atom rings -184: testing bond rings -184: searching atom rings -184: searching bond rings -184: done -226/235 Test #184: pySubstructLibrary ..................... Passed 36.13 sec -146: [05:52:18] --------------------------------- -146: [05:52:18] test github issue 256: handling of zero-atom molecules +170: [15:24:50] Timed out after 71 seconds. +146: [15:25:04] done +146: [15:25:04] --------------------------------- +146: [15:25:04] test github issue 256: handling of zero-atom molecules 146: -146: [05:52:18] --------------------------------- -146: [05:52:18] test embedder callback function -146: [05:52:18] --------------------------------- -146: [05:52:18] test multi-threaded multi-conf embedding +146: [15:25:04] --------------------------------- +146: [15:25:04] test embedder callback function +146: [15:25:04] --------------------------------- +146: [15:25:04] test multi-threaded multi-conf embedding 146: -146: [05:52:20] --------------------------------- -146: [05:52:20] test github issue 563: Incorrect ring stereochemistry after embedding +146: [15:25:11] --------------------------------- +146: [15:25:11] test github issue 563: Incorrect ring stereochemistry after embedding 146: 146: CNC[C@H]1CC[C@H](C[NH3+])CC1 -33: [05:52:21] Finished -33: [05:52:21] ------------------------------------- -33: [05:52:21] Test github1843: RWMol.clear() should not destroy ring pointer. -33: [05:52:21] Finished -33: [05:52:21] ------------------------------------- -33: [05:52:21] Test Github 6370: non-physical radical counts being preserved -33: [05:52:21] Finished -227/235 Test #33: graphmolTest1 .......................... Passed 76.21 sec -146: [05:52:21] --------------------------------- -146: [05:52:21] test github issue 568: Incorrect stereochemistry after embedding +209: [15:25:12] Explicit valence for atom # 0 Br, 1, is greater than permitted +209: =============================================================================== +209: All tests passed (38344 assertions in 51 test cases) +209: +227/235 Test #209: molStandardizeCatchTest ................ Passed 50.47 sec +146: [15:25:13] --------------------------------- +146: [15:25:13] test github issue 568: Incorrect stereochemistry after embedding 146: 146: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 146: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 146: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 146: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 146: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O +33: [15:25:16] Finished +33: [15:25:16] ------------------------------------- +33: [15:25:16] Test github1843: RWMol.clear() should not destroy ring pointer. +33: [15:25:16] Finished +33: [15:25:16] ------------------------------------- +33: [15:25:16] Test Github 6370: non-physical radical counts being preserved +33: [15:25:16] Finished +228/235 Test #33: graphmolTest1 .......................... Passed 131.73 sec 146: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 146: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O @@ -35288,24 +35325,12 @@ 146: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 146: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 146: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 -209: [05:52:28] Explicit valence for atom # 0 Br, 1, is greater than permitted -209: =============================================================================== -209: All tests passed (38344 assertions in 51 test cases) -209: -228/235 Test #209: molStandardizeCatchTest ................ Passed 25.74 sec 146: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 146: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 146: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 146: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 -146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 -146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 -146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 -146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 -146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 -146: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 -146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 -147: [05:52:34] Interrupted, cancelling conformer generation +147: [15:25:27] Interrupted, cancelling conformer generation 147: Atoms: 147: 0 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[9 3 1 6] 147: 1 6 C chg: 0 deg: 4 exp: 4 imp: 0 hyb: SP3 chi: CCW nbrs:[0 13 6 7] @@ -35338,12 +35363,23 @@ 147: 13 7->5 order: 1 147: 14 8->12 order: a conj?: 1 aromatic?: 1 147: 15 11->2 order: 1 stereo: CCW bonds: (9 4 5) conj?: 1 +146: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 147: =============================================================================== 147: All tests passed (12742 assertions in 21 test cases) 147: -229/235 Test #147: distGeomHelpersCatch ................... Passed 76.50 sec -146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 -146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] +229/235 Test #147: distGeomHelpersCatch ................... Passed 127.77 sec +173: Query 3 +171: =============================================================================== +171: All tests passed (93 assertions in 5 test cases) +171: +230/235 Test #171: testRascalCluster ...................... Passed 118.08 sec +146: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 +173: Query 4 +146: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 +146: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 +146: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 +146: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 +146: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 235: DbCLI/UnitTestDbCLI.py ............ [100%] 235: 235: =============================== warnings summary =============================== @@ -35352,64 +35388,60 @@ 235: decBase = declarative_base() 235: 235: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html -235: ======================== 12 passed, 1 warning in 26.40s ======================== -146: [05:52:39] Molecule does not have explicit Hs. Consider calling AddHs() -146: [05:52:36] --------------------------------- -146: [05:52:36] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system -146: [05:52:36] --------------------------------- -146: [05:52:36] More ChEMBL molecules failing bounds smoothing. -146: [05:52:36] --------------------------------- -146: [05:52:36] ugly conformations can be generated for highly constrained ring systems. -146: [05:52:36] --------------------------------- -146: [05:52:36] test embed parameters structure. -146: [05:52:36] --------------------------------- -146: [05:52:36] test github 1227: Hs being used in RMSD filtering. -146: [05:52:36] --------------------------------- -146: [05:52:36] Failure to embed larger aromatic rings. -146: [05:52:37] --------------------------------- -146: [05:52:37] Deterministic with large random seeds -146: [05:52:38] --------------------------------- -146: [05:52:38] Github #1990: seg fault after RemoveHs -146: [05:52:38] --------------------------------- -146: [05:52:38] Github #2246: Use coordMap when starting embedding from random coords -146: [05:52:39] --------------------------------- -146: [05:52:39] Providing a distance bounds matrix. -146: [05:52:39] --------------------------------- -146: [05:52:39] Disabling fragmentation. -146: [05:52:39] --------------------------------- -146: [05:52:39] Using symmetry in conformation pruning. -146: [05:52:39] --------------------------------- -146: [05:52:39] Force trans amides. -146: [05:52:39] --------------------------------- -146: [05:52:39] test missing Hs warning. -146: [05:52:39] --------------------------------- -146: [05:52:39] basic H bond support. -146: [05:52:39] ******************************************************* -230/235 Test #146: testDistGeomHelpers .................... Passed 82.27 sec -231/235 Test #235: pythonProjectTests ..................... Passed 27.33 sec -171: =============================================================================== -171: All tests passed (93 assertions in 5 test cases) -171: -232/235 Test #171: testRascalCluster ...................... Passed 71.68 sec -173: Query 3 -173: Query 4 +235: ======================== 12 passed, 1 warning in 50.23s ======================== +231/235 Test #235: pythonProjectTests ..................... Passed 51.60 sec +146: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 +146: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] +146: [15:25:39] Molecule does not have explicit Hs. Consider calling AddHs() +146: [15:25:33] --------------------------------- +146: [15:25:33] test github issue 696: Bad 1-4 bounds matrix elements in highly constrained system +146: [15:25:33] --------------------------------- +146: [15:25:33] More ChEMBL molecules failing bounds smoothing. +146: [15:25:33] --------------------------------- +146: [15:25:33] ugly conformations can be generated for highly constrained ring systems. +146: [15:25:33] --------------------------------- +146: [15:25:33] test embed parameters structure. +146: [15:25:33] --------------------------------- +146: [15:25:33] test github 1227: Hs being used in RMSD filtering. +146: [15:25:33] --------------------------------- +146: [15:25:33] Failure to embed larger aromatic rings. +146: [15:25:36] --------------------------------- +146: [15:25:36] Deterministic with large random seeds +146: [15:25:37] --------------------------------- +146: [15:25:37] Github #1990: seg fault after RemoveHs +146: [15:25:37] --------------------------------- +146: [15:25:37] Github #2246: Use coordMap when starting embedding from random coords +146: [15:25:39] --------------------------------- +146: [15:25:39] Providing a distance bounds matrix. +146: [15:25:39] --------------------------------- +146: [15:25:39] Disabling fragmentation. +146: [15:25:39] --------------------------------- +146: [15:25:39] Using symmetry in conformation pruning. +146: [15:25:39] --------------------------------- +146: [15:25:39] Force trans amides. +146: [15:25:39] --------------------------------- +146: [15:25:39] test missing Hs warning. +146: [15:25:39] --------------------------------- +146: [15:25:39] basic H bond support. +146: [15:25:39] ******************************************************* +232/235 Test #146: testDistGeomHelpers .................... Passed 139.61 sec +173: Query 5 170: =============================================================================== 170: All tests passed (3582 assertions in 34 test cases) 170: -233/235 Test #170: testRascalMCES ......................... Passed 79.14 sec -173: Query 5 +233/235 Test #170: testRascalMCES ......................... Passed 133.15 sec 173: =============================================================================== 173: All tests passed (215 assertions in 18 test cases) 173: -234/235 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 107.56 sec -5: [06:09:00] Finished: testMultipleTimes() -5: [06:09:00] +234/235 Test #173: testSynthonSpaceSubstructureSearch ..... Passed 148.91 sec +5: [15:41:31] Finished: testMultipleTimes() +5: [15:41:31] 5: ----------------------------------------- -235/235 Test #5: testConcurrentQueue .................... Passed 1076.58 sec +235/235 Test #5: testConcurrentQueue .................... Passed 1108.67 sec 100% tests passed, 0 tests failed out of 235 -Total Test time (real) = 1076.83 sec +Total Test time (real) = 1109.34 sec make[2]: Leaving directory '/build/reproducible-path/rdkit-202409.6/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/rdkit-202409.6' create-stamp debian/debhelper-build-stamp @@ -38060,37 +38092,37 @@ diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged -dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol MemoryContextAllocZero: it's probably a plugin +dpkg-shlibdeps: warning: debian/postgresql-17-rdkit/usr/lib/postgresql/17/lib/rdkit.so contains an unresolvable reference to symbol errfinish: it's probably a plugin dpkg-shlibdeps: warning: 24 other similar warnings have been skipped (use -v to see them all) -dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_IndexError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_IsTrue used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyErr_SetString used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_KeyError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries -dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyExc_ValueError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyExc_RuntimeError used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyObject_CallFunction used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyErr_SetObject used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries +dpkg-shlibdeps: warning: symbol PyLong_FromUnsignedLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_NoneStruct used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries +dpkg-shlibdeps: warning: symbol _Py_Dealloc used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: symbol PyLong_FromLong used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2024.09.6 found in none of the libraries dpkg-shlibdeps: warning: 2 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined +dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.6-2_arm64.deb'. -dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.6-2_all.deb'. dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202409.6-2_arm64.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202409.6-2_arm64.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.6-2_arm64.deb'. +dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202409.6-2_all.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202409.6-2_arm64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202409.6-2_all.deb'. +dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202409.6-2_arm64.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202409.6-2_arm64.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202409.6-2_arm64.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202409.6-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202409.6-2_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202409.6-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -38098,12 +38130,14 @@ 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/2068256/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2068256/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/2513156 and its subdirectories -I: Current time: Sun Mar 9 06:14:02 -12 2025 -I: pbuilder-time-stamp: 1741544042 +I: removing directory /srv/workspace/pbuilder/2068256 and its subdirectories +I: Current time: Sun Apr 12 15:50:17 +14 2026 +I: pbuilder-time-stamp: 1775958617